Identification of novel e2f target genes and use thereof

ABSTRACT

The present invention concerns a method for altering characteristics of a plant. The invention describes the identification of genes that are upregulated or downregulated in transgenic plants overexpressing E2Fa/DPa and the use of such sequences to alter plant characteristics. A preferred way for altering characteristics of a plant comprises modifying expression of one or more nucleic acid sequences and or modifying level and/or activity of one or more proteins, which nucleic acids and/or proteins are essentially similar to any one or more of SEQ ID NO 1 to 2755. Some of the genes identified in the present invention have an E2Fa target consensus sequence in their 5′ upstream region. The identified genes play a role in a variety of biological processes, such as DNA replication, cell wall biosynthesis, nitrogen and/or carbon metabolism, transcription factors etc.

The present invention concerns altering plant characteristics. Moreparticularly, the present invention relates to identification of genesand proteins involved in E2Fa/DPa-mediated processes and further relatesto use of such genes and proteins for altering characteristics inplants.

The present invention concerns a method for altering one or more plantcharacteristics, whereby the altered plant characteristic is selectedfrom altered development, altered plant growth, altered, for exampleincreased, plant yield and/or biomass, biochemistry, physiology,architecture, metabolism, survival capacity or stress tolerance bymodifying expression of one or more of the genes according to thepresent invention and/or by modifying levels and/or activity of theproteins encoded by these genes. The present invention also concernsgenetic constructs for performing the methods of the invention and toplants or plant parts obtainable by the methods of the presentinvention, which plants have altered characteristics compared to theirotherwise isogenic counterparts. The invention also extends torecombinant nucleic acids and the use thereof in the methods accordingto the invention.

Growth, development and differentiation of higher organisms arecontrolled by a highly ordered set of events called the cell cycle(Morgan, 1997). Cell division and cell growth are operated by the cellcycle, which ensures correct timing and high fidelity of the differenttransition events involved. Cell cycle regulation at both G1→S and G2→Mphase transitions depends on the formation of appropriate proteincomplexes and both transitions are believed to be the major controlpoints in the cell cycle. The cell's decision to proliferate andsynthesize DNA and ultimately to divide is made at the G1→S restrictionpoint in late G1. Overcoming this point of no return requires the cell'scompetence to initiate DNA synthesis as well as the expression ofS-phase genes. Transcription of S-phase-specific genes requires bindingto the DNA of an E2F transcription factor. Dimerisation of E2F with DPis a prerequisite for high affinity binding to the E2F consensus DNAbinding site (A/T)TT(G/C)(G/C)C(G/C)(G/C) (SEQ ID NO 2775), for example(TTT(C/G)(C/G)CGC), that can be found in the promoters of genes involvedin DNA replication, repair, checkpoint control and differentiation (Renet al., 2002; Weinmann et al., 2001; Kel et al., 2001). Variants of thisconsensus sequence as well as other locations of this consensussequences are also found. The heterodimeric E2F/dimerization partner(DP) transcription factor also regulates the promoter activity ofmultiple genes, which are essential for DNA replication and cell cyclecontrol (Helin, 1998; Müller and Helin, 2000). E2F transcription factorsare critical effectors of the decision to pass the restriction point andto allow the cell to proceed in S-phase.

In the Arabidopsis genome, 3 E2F (E2Fa, E2Fb, and E2Fc) and 2 DP genes(DPa and DPb) are present (Vandepoele et al., 2002). The phenotypicanalysis of plants overexpressing E2Fa and DPa was described recently(De Veylder et al., 2002). Microscopic analysis revealed that E2Fa/DPaoverproducing cells underwent ectopic cell division orendoreduplication, depending on the cell type. Whereas extra celldivisions resulted in cells being smaller than those seen in the sametissues of control plants, extra endoreduplication caused formation ofgiant nuclei. RT-PCR demonstrated that expression levels of genesinvolved in DNA replication (CDC6, ORC1, MCM, DNA pol α) were stronglyupregulated in plants overexpressing E2Fa and DPa (De Veylder et al.,2002).

The present invention provides genes having altered expression levels inplants overexpressing E2Fa and DPa relative to expression levels incorresponding wild type plants. Furthermore, the present inventionprovides means to modulate expression of these genes, which in turnallows for modulation of the biological processes that they control. Thepresent invention provides methods to mimic E2F/DP level and/or activityby manipulating downstream factors involved in E2F/DP pathways. Thisstrategy allows a fine-tuning of the effects of E2Fa/DPa. Whereasoverexpression of E2Fa or DPa or both can be pleiotropic and/or can havepleiotropic effects, it is the invention provides methods to alter plantcharacteristics in a more controlled and targeted way, by using theE2F/DP target genes as defined by the present invention. Modulation ofparticular biological processes is now possible and may give rise toplants having altered characteristics, which may have particularlyuseful applications in agriculture and horticulture.

Therefore, according to the present invention, there is provided amethod to alter one or more plant characteristics, comprising modifying,in a plant, expression of one or more nucleic acids and/or modifyinglevel and/or activity of one or more proteins, which nucleic acids orproteins are essentially similar to any one of SEQ ID NO 1 to 2755, andwherein said one or more plant characteristics are altered relative tocorresponding wild type plants.

The inventors designed a microarray experiment, comparing transcriptlevels of more than 4579 genes of wild type and transgenic Arabidopsislines overexpressing E2Fa/DPa. Surprisingly, the inventors found thatparticular genes are up or down regulated in E2Fa-DPa overexpressingplants. The sequences which were at least 1.3 times upregulated ordownregulated, are represented with their MIPS (Munich informationcenter for protein sequences) accession number MATDB databasehttp://mips.gsf.de/proj/thal/db/index.html) in Tables 4 and 5. Sequenceswhich were at least 2-fold upregulated or 2-fold downregulated are shownin Tables 1 and 2, respectively. Further classification of these genesaccording to their function is provided in Tables 1 and 2. Promoteranalysis of these genes allowed for the identification of genes underthe direct control of E2Fa and/or DPa proteins and genes that areindirectly controlled by the E2Fa/DPa complex. Examples of mechanismsfor such indirect control include, (i) recognition by E2F/DP of othersequence elements that diverge from the consensus recognition site; (ii)possible association of E2F/DP with other DNA binding proteins capableof recognizing other DNA elements; and (iii) sequential transcriptionactivation of a first gene capable of regulating transcription of asecond gene. It is to be understood that having an E2F target sequenceis not a prerequisite to be regulated by E2F.

The gene that corresponds to the sequence deposited under the MIPSdatabase accession number At1g57680 is an example of a gene, which islikely to be indirectly controlled by the E2Fa/DPa complex. This gene isof unknown function. It was surprising to find this unknown gene and theother genes of Tables 1, 2, 4 and 5 to be involved in E2Fa/DPacontrolled processes. The genes according to the present invention arerepresented herein with their nucleic acid sequence and correspondingamino acid sequence as set forth in SEQ ID NO 1 to 2755.

Preferably expression and/or level and/or activity of one of the genesand/or proteins according to any of SEQ ID NO 1 to 2755 is modified.Alternatively expression and/or level and/or activity of one or more ofthose genes and/or proteins is modified. According to a furtherembodiment one or more gene/and or proteins of the same functionalcategory as presented in Table 1 or Table 2, are modified.

The term “modifying expression” relates to altering level (increasingexpression or decreasing expression) or altering the time or alteringthe place of expression of a nucleic acid. The term “modified” as usedherein is used interchangeably with “altered” or “changed”.

Modified expression (or level or activity) of a sequence essentiallysimilar to any one of SEQ ID NO 1 to 2755 encompasses changed expression(or level or activity) of a gene product, namely a polypeptide, inspecific cells or tissues. The changed expression, activity and/orlevels are changed compared to expression, activity and/or levels of thegene or protein essentially similar to any one of SEQ ID NO 1 to 2755acid in corresponding wild-type plants. The changed gene expression mayresult from changed expression levels of an endogenous gene essentiallysimilar to any one of SEQ ID NO 1 to 2755 acid and/or may result fromchanged expression levels of a gene essentially similar to SEQ ID NO 1to 2755 acid previously introduced into a plant. Similarly, changedlevels and/or activity of a protein essentially similar to any one ofSEQ ID NO 1 to 2755 acid may be due to changed expression of anendogenous nucleic acid/gene and/or due to changed expression of nucleicacid/gene previously introduced into a plant.

Modified expression of a gene/nucleic acid and/or increasing ordecreasing activity and/or levels of a gene product may be effected, forexample, by chemical means and/or recombinant means.

Advantageously, modified expression of a nucleic acid according to theinvention and/or modified activity and/or levels of a protein accordingto the invention may be effected by chemical means, i.e. by exogenousapplication of one or more compounds or elements capable of modifyingactivity and/or levels of the protein and/or capable of modifyingexpression of a nucleic acid/gene according to the invention. The term“exogenous application” as defined herein is taken to mean thecontacting or administering of a suitable compound or element to plantcells, tissues, organs or to the whole organism. The compound or elementmay be exogenously applied to a plant in a form suitable for plantuptake (such as through application to the soil for uptake via theroots, or in the case of some plants by applying directly to the leaves,for example by spraying). The exogenous application may take place onwild-type plants or on transgenic plants that have previously beentransformed with a nucleic acid/gene according to the present inventionor with another transgene.

Suitable compounds or elements include proteins or nucleic acidsaccording to SEQ ID NO 1 to 2755 or proteins or nucleic acidsessentially similar to SEQ ID NO 1 to 2755. Essentially similar proteinsor nucleic acids are, homologues, derivatives or active fragments ofthese proteins and/or portions or sequences capable of hybridizing withthese nucleic acids. The exogenous application of yet other compounds orelements capable of modifying levels of factors that directly orindirectly activate or inactivate a protein according to the presentinvention will also be suitable in practicing the invention. Thesecompounds or elements also include antibodies that can recognize ormimic the function of the proteins according to the present invention.Such antibodies may comprise “plantibodies”, single chain antibodies,IgG antibodies and heavy chain camel antibodies, as well as fragmentsthereof. Additionally or alternatively, the resultant effect may also beachieved by the exogenous application of an interacting protein oractivator or an inhibitor of the gene/gene product according to thepresent invention. Additionally or alternatively, the compound orelement may be a mutagenic substance, such as a chemical selected fromany one or more of: N-nitroso-N-ethylurea, ethylene imine, ethylmethanesulphonate and diethyl sulphate. Mutagenesis may also be achievedby exposure to ionising radiation, such as X-rays or gamma-rays orultraviolet light. Methods for introducing mutations and for testing theeffect of mutations (such as by monitoring gene expression and/orprotein activity) are well known in the art.

Therefore, according to one aspect of the present invention, there isprovided a method for altering plant characteristics, comprisingexogenous application of one or more compounds or elements capable ofmodifying expression of a gene and/or capable of modifying activityand/or levels of a protein according to the present invention.

Additionally or alternatively, and according to a preferred embodimentof the present invention, modified of expression of a nucleic acidand/or modified of activity and/or levels of a protein, wherein thesenucleic acids or proteins are essentially similar to any of SEQ ID NO 1to 2755, may be effected by recombinant means. Such recombinant meansmay comprise a direct and/or indirect approach for modifying expressionof a nucleic acid and/or for modifying activity and/or levels of aprotein.

Therefore there is provided by the present invention, a method to alterplant characteristics, comprising modifying gene expression and/orprotein levels and/or protein activity, which modification may beeffected by recombinant means and/or by chemical means and wherein saidgene and/or protein are essentially similar to any one of SEQ ID NO 1 to2755.

An indirect recombinant approach may comprise for example introducing,into a plant, a nucleic acid capable of increasing or decreasingactivity and/or levels of the protein in question (a protein essentiallysimilar to any one of SEQ ID NO 1 to 2755) and/or capable of increasingor decreasing expression of the gene in question (a gene essentiallysimilar to any one of SEQ ID NO 1 to 2755). Examples of such nucleicacids to be introduced into a plant, are nucleic acids encodingtranscription factors or activators or inhibitors that bind to thepromoter of a gene or that interact with a protein essentially similarto any one of SEQ ID NO 1 to 2755. Methods to test these types ofinteractions and methods for isolating nucleic acids encoding suchinteractors include yeast one-hybrid or yeast two-hybrid screens.

Also encompassed by an indirect approach for modifying activity and/orlevels of a protein according to the present invention and/or expressionof a gene according to the present invention, is the provision of aregulatory sequence, or the inhibition or stimulation of regulatorysequences that drive expression of the native gene in question or of thetransgene in question. Such regulatory sequences may be introduced intoa plant. For example, the nucleic acid introduced into the plant is apromoter, capable of driving the expression of the endogenous geneessentially similar to any one of SEQ ID NO 1 to 2755.

A further indirect approach for modifying activity and/or levels and/orexpression of a gene or protein according to the present invention in aplant encompasses modifying levels in a plant of a factor able tointeract with the protein according to the present invention. Suchfactors may include ligands of the protein according to the presentinvention. Therefore, the present invention provides a method foraltering characteristics of a plant, when compared to the correspondingwild-type plants, comprising modifying expression of a gene coding for aprotein which is a natural ligand of a protein essentially similar toany one of SEQ ID NO 1 to 2755. Furthermore, the present invention alsoprovides a method to alter one or more plant characteristics relative tocorresponding wild-type plants, comprising modifying expression of agene coding for a protein which is a natural target/substrate of aprotein essentially similar to SEQ ID NO 1 to 2755.

A direct and more preferred approach to alter one or more plantcharacteristics, comprises introducing into a plant a nucleic acidessentially similar to any one of SEQ ID NO 1 to 2755, wherein saidnucleic acid essentially similar to any one of SEQ ID NO 1 to 2755 isany one of SEQ ID NO 1 to 2755 or a portion thereof or sequences capableof hybridizing therewith and which nucleic acid preferably encodes aprotein essentially similar to any one of SEQ ID NO 1 to 2755, whichprotein essentially similar to any one of SEQ ID NO 1 to 2755 is any oneof SEQ ID NO 1 to 2755 or a homologue, derivative or active fragmentthereof. The nucleic acid may be introduced into a plant by, forexample, transformation.

In the context of the present invention the term “modifying expression”and modifying level and/or activity encompasses “enhancing ordecreasing”. Methods for obtaining enhanced or increased expression ofgenes or gene products are well documented in the art and are forexample overexpression driven by a strong promoter, the use oftranscription enhancers or translation enhancers. The term“overexpression” of a gene refers to expression patterns and/orexpression levels of said gene normally not occurring under naturalconditions. Ectopic expression can be achieved in a number of waysincluding operably linking of a coding sequence encoding said protein toan isolated homologous or heterologous promoter in order to create achimeric gene.

Alternatively and/or additionally, increased expression of a gene orincreased activities and/or levels of a protein in a plant cell, isachieved by mutagenesis. For example these mutations can be responsiblefor the changed control of the gene, resulting in more expression of thegene; relative to the wild-type gene. Mutations can also causeconformational changes in a protein, resulting in more activity and/orlevels of the protein.

Examples of decreasing expression of a gene are also well documented inthe art and include for example: downregulation of expression byanti-sense techniques, RNAi techniques, small interference RNAs(siRNAs), microRNA (miRNA), etc. Therefore according to a particularaspect of the invention, there is provided a method to altercharacteristics of plants, including technologies that are based on forexample the synthesis of antisense transcripts, complementary to themRNA of a gene essentially similar to any one of SEQ ID NO 1 to 2755.

Another method for downregulation of gene expression or gene silencingcomprises use of ribozymes, for example as described in WO9400012(Atkins et al.), WO9503404 (Lenee et al.), WO0000619 (Nikolau et al.),WO9713865 (Ulvskov et al.) and WO9738116 (Scott et al.).

Gene silencing may also be achieved by insertion mutagenesis (forexample, T-DNA insertion or transposon insertion) or by gene silencingstrategies as described among others in the documents WO9836083(Baulcombe and Angell), WO9853083 (Grierson et al.), WO9915682(Baulcombe et al.) or WO9953050 (Waterhouse et al.).

Expression of an endogenous gene may also be reduced if the endogenousgene contains a mutation. Such a mutant gene may be isolated andintroduced into the same or different plant species in order to obtainplants having altered characteristics. Also dominant negative mutants ofa nucleic acid essentially similar to any one of SEQ ID NO 1 to 2755 canbe introduced in the cell to decrease the level/and or activity of theendogenous corresponding protein.

Other methods to decrease the expression of a nucleic acid and/oractivity and/or level of proteins essentially similar to any one of SEQID NO 1 to 2755 in a cell encompass, for example, the mechanisms oftranscriptional gene silencing, such as the methylation of the promoterof a gene according to the present invention.

Modifying expression of the gene also encompasses altered transcriptlevel of the gene. Altered transcript levels of a gene can be sufficientto induce certain phenotypic effects, for example via the mechanism ofcosuppression. Here the overall effect of overexpression of a transgeneis that there is less level and/or activity in the cell of the protein,which is encoded by the native gene showing homology to the introducedtransgene.

Cosuppression is accomplished by the addition of coding sequences orparts thereof in a sense orientation into the cell. Therefore, accordingto one aspect of the present invention, the characteristics of a plantmay be changed by introducing into a plant an additional copy (in fullor in part) of a gene essentially similar to any one of SEQ ID NO 1 to2755 already present in a host plant. The additional gene may silencethe endogenous gene, giving rise to a phenomenon known asco-suppression.

According to the invention, “nucleic acid” or the “gene” essentiallysimilar to any one of SEQ ID NO 1 to 2755 in a plant may be the wildtype gene, i.e. native or endogenous or heterologous, i.e. derived fromanother individual plant or plant species. The gene (transgene) may besubstantially modified from its native form in composition and/orgenomic environment through deliberate human manipulation. Thistransgene can be introduced into a host cell by transformationtechniques. Also expression of the native genes can be modified byintroduction in the plant of regulatory sequences capable of alteringexpression of the native gene, as described above.

The term “modifying activity” relates to enhancing, decreasing oraltering time or place of activity of a protein or polypeptide.According to the invention, the “protein” or the “polypeptide” may bethe wild type protein, i.e. native or endogenous, or alternatively, theprotein may be heterologous, i.e. derived from another individual orspecies.

The term “essentially similar to” in relation to a protein of thepresent invention as used herein includes variants such as homologues,derivatives and functional fragment thereof. The term “essentiallysimilar to” in relation to a gene includes variants such as at least apart of the gene in question; a complement of the gene; RNA, DNA, a cDNAor a genomic DNA corresponding to the protein or gene; a variant of thegene due to the degeneracy of the genetic code; a family member of thegene or protein; an allelic variant of the gene or protein; anddifferent splice variant of the gene or protein and variants that areinterrupted by one or more intervening sequences. Advantageously,nucleic acids or proteins essentially similar to nucleic acids and theproteins according to any of SEQ ID NO 1 to 2755 may be used in themethods of the present invention. These variant nucleic acids andvariant amino acids are described further below.

Any variant of a particular protein according to the present inventionis a variant, which upon construction of a phylogenetic tree with thatparticular protein, tends to cluster around the particular protein whichis any one of SEQ ID NO 1 to 2755. Such a phylogenetic tree can beconstructed with alignments of amino acid sequences or with nucleic acidsequences. A person skilled in the art could readily determine whetherany variant in question falls within the definition of a “a nucleic acidor protein essentially similar to any one of SEQ ID NO 1 to 2755”.Hereto the man skilled in the art would use known techniques andsoftware for the making of such phylogenetic trees, such as a GCG, EBIor CLUSTAL package, or Align X, using default parameters.Advantageously, the methods according to the present invention may alsobe practised using such variants.

Any variant suitable for use in the methods according to the inventionmay readily be determined using routine techniques, such as by followingthe methods described in the Examples section by simply substituting thesequence used in the actual Example with the fragment to be tested forfunctionality.

A first example of such variants are “homologues” of the proteins of thepresent invention, which homologues encompass peptides, oligopeptides,polypeptides, proteins and enzymes having amino acid substitutions,deletions and/or additions relative to the protein in question andhaving similar biological and functional activity as an unmodifiedprotein from which they are derived. To produce such homologues, aminoacids of the protein may be replaced by other amino acids having similarproperties (such as similar hydrophobicity, hydrophilicity,antigenicity, propensity to form or break α-helical structures orβ-sheet structures). Conservative substitution tables are well known inthe art (see for example Creighton (1984).

The homologues useful in the method according to the invention may haveat least 30%, 32%, 34%, 36%, 38%, 40%, 42%, 44%, 46%, 48% or 50%sequence identity or similarity (functional identity) to the unmodifiedprotein, alternatively at least 52%, 54%, 56%, 58% or 60% sequenceidentity or similarity to an unmodified protein, or alternatively atleast 62%, 64%, 66%, 68% or 70% sequence identity or similarity to anunmodified protein. Typically, the homologues have at least 72%, 74%,76%, 78% or 80% sequence identity or similarity to an unmodifiedprotein, preferably at least 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88% or89% sequence identity or similarity, further preferably at least 90%,91%, 92%, 93% or 94% sequence identity or similarity to an unmodifiedprotein, further preferably at least 95% 96%, 97%, 98% or 99% sequenceidentity or similarity to an unmodified protein. This % identity can becalculated using the Gap program in the WISCONSIN PACKAGE version10.0-UNIX from Genetics Computer Group, Inc based on the method ofNeedleman and Wunsch (J. Mol. Biol. 48:443-453 (1970)) using the set ofdefault parameters for pairwise comparison (for amino acid sequencecomparison: Gap Creation Penalty=8, Gap Extension Penalty=2; fornucleotide sequence comparison: Gap Creation Penalty=50; Gap ExtensionPenalty=3).

The percentage of identity can also be calculated by using otheralignment program well known in the art. For example, the percentage ofidentity can be calculated using the program needle (EMBOSS package) orstretcher (EMBOSS package) or the program align X, as a module of thevector NTI suite 5.5 software package, using the parameters (for exampleGAP penalty 5, GAP opening penalty 15, GAP extension penalty 6.6).

These above-mentioned analyses for comparing sequences may be done onfull-length sequences but additionally or alternatively the calculationof sequence identity or similarity can be based on a comparison ofcertain regions such as conserved domains.

The identification of such domains, would also be well within the realmof a person skilled in the art and involves, for example, running acomputer readable format of the nucleic acids of the present inventionin alignment software programs, scanning publicly available informationon protein domains, conserved motifs and boxes. This type of informationon protein domains is available in the PRODOM(http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/prodomsrchjj.html), PIR(http://pir.georgetown.edu/), INTERPRO (http://www.ebi.ac.uk/interpro/)or pFAM (http://pfam.wustl.edu/) database. Sequence analysis programsdesigned for motif searching can be used for identification offragments, regions and conserved domains as mentioned above. Preferredcomputer programs would include but are not limited to: MEME,SIGNALSCAN, and GENESCAN. A MEME algorithm (Version 2.2) can be found inversion 10.0 of the GCG package; or on the Internet sitehttp://www.sdsc.edu/MEME/meme. SIGNALSCAN version 4.0 information isavailable on the Internet sitehttp://biosci.cbs.umn.edu/software/sigscan.html. GENESCAN can be foundon the Internet site http://gnomic.stanford.edu/GENESCANW.html.

As mentioned above the nucleic acid suitable for practising the methodsof the present invention can be wild type (native or endogenous).Alternatively, the nucleic acid may be derived from another (or thesame) species, which gene is introduced into the plant as a transgene,for example by transformation. The nucleic acid may thus be derived(either directly or indirectly (if subsequently modified)) from anysource provided that the nucleic acid, when expressed in a plant, leadsto modified expression of a nucleic acid/gene or modified activityand/or levels of a protein essentially similar to SEQ ID NO 1 to 2755.The nucleic acid may be isolated from a microbial source, such asbacteria, yeast or fungi, or from a plant, algae, insect, or animal(including human) source. Methods for the search and identification ofother homologues of the proteins of the present invention, or fornucleic acid sequences encoding homologues of proteins of the presentinvention would be well known to person skilled in the art. Methods forthe alignment of sequences for comparison are well known in the art,such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. The BLASTalgorithm calculates percent sequence identity and performs astatistical analysis of the similarity between the two sequences. Thesoftware for performing BLAST analysis is publicly available through theNational Center for Biotechnology Information.

Two special forms of homology, orthologous and paralogous, areevolutionary concepts used to describe ancestral relationships of genes.The term “paralogous” relates to gene-duplications within the genome ofa species leading to paralogous genes. The term “orthologous” relates tohomologous genes in different organisms due to ancestral relationship.The term “homologues” as used herein also encompasses paralogues andorthologues of the proteins used in the methods according to theinvention.

A preferred homologue is a homologue obtained from a plant, whether fromthe same plant species or different. The nucleic acid may be isolatedfrom a dicotyledonous species, preferably from the family Brassicaceae,further preferably from Arabidopsis thaliana.

Suitable homologues for use in the methods of the present invention havebeen identified in the genomes of rice and maize. These homologues arerepresented by their Genbank accession numbers in Table 1 and 2. Otherhomologues, especially orthologues from other plant species, areidentifiable by methods well known by a person skilled in the art. Insilico, methods involve running sequence alignment programs with thesequence of interest as mentioned above. In vivo methods involve the DNAencoding the protein of interest and are for example PCR techniquesusing degenerated primers designed based on the sequence of interest,which is any one essentially similar to any one of SEQ ID NO 1 to 2755,or hybridisation techniques with at least part of the sequence ofinterest.

“Substitutional variants” of a protein are those in which at least oneresidue in an amino acid sequence has been removed and a differentresidue inserted in its place. Amino acid substitutions are typically ofsingle residues, but may be clustered depending upon functionalconstraints placed upon the polypeptide; insertions will usually be ofthe order of about 1-10 amino acid residues, and deletions will rangefrom about 1-20 residues.

“Insertional variants” of a protein are those in which one or more aminoacid residues are introduced into a predetermined site in the protein.Insertions can comprise amino-terminal and/or carboxy-terminal fusionsas well as intra-sequence insertions of single or multiple amino acids.Generally, insertions within the amino acid sequence will be smallerthan amino- or carboxy-terminal fusions, of the order of about 1 to 10residues. Examples of amino- or carboxy-terminal fusion proteins orpeptides include the binding domain or activation domain of atranscriptional activator as used in the yeast two-hybrid system, phagecoat proteins, (histidine)₆-tag, glutathione S-transferase-tag, proteinA, maltose-binding protein, dihydrofolate reductase, Tag•100 epitope,c-myc epitope, FLAG®-epitope, lacZ, CMP (calmodulin-binding peptide), HAepitope, protein C epitope and VSV epitope.

“Deletion variants” of a protein are characterized by the removal of oneor more amino acids from the protein. Amino acid variants of a proteinmay readily be made using peptide synthetic techniques well known in theart, such as solid phase peptide synthesis and the like, or byrecombinant DNA manipulations. The manipulation of DNA sequences toproduce substitution, insertion or deletion variants of a protein arewell known in the art. For example, techniques for making substitutionmutations at predetermined sites in DNA are well known to those skilledin the art and include M13 mutagenesis, T7-Gen in vitro mutagenesis(USB, Cleveland, Ohio), QuickChange Site Directed mutagenesis(Stratagene, San Diego, Calif.), PCR-mediated site-directed mutagenesisor other site-directed mutagenesis protocols.

The term “derivatives” of a protein according to the present inventionare those peptides, oligopeptides, polypeptides, proteins and enzymeswhich may comprise substitutions, deletions or additions of naturallyand non-naturally occurring amino acid residues compared to the aminoacid sequence of a naturally-occurring form of the protein as depositedunder the accession numbers presented in Table 1, 2, 4 and 5.“Derivatives” of a protein of the present invention encompass peptides,oligopeptides, polypeptides, proteins and enzymes which may comprisenaturally occurring altered, glycosylated, acylated or non-naturallyoccurring amino acid residues compared to the amino acid sequence of anaturally-occurring form of the polypeptide. A derivative may alsocomprise one or more non-amino acid substituents compared to the aminoacid sequence from which it is derived, for example a reporter moleculeor other ligand, covalently or non-covalently bound to the amino acidsequence such as, for example, a reporter molecule which is bound tofacilitate its detection, and non-naturally occurring amino acidresidues relative to the amino acid sequence of a naturally-occurringprotein of the present invention.

Another variant useful in the methods of the present invention is anactive fragment of a protein essentially similar to any one of SEQ ID NO1 to 2755. The expression “functional fragment” in relation to a proteinrefers to a fragment that encompasses contiguous amino acid residues ofsaid protein, and that has retained the biological activity of saidnaturally-occurring protein. For example, useful fragments comprise atleast 10 contiguous amino acid residues of a protein essentially similarto any one of SEQ ID NO 1 to 2755. Other preferred fragments arefragments of these proteins starting at the second or third or furtherinternal methionin residues. These fragments originate from proteintranslation, starting at internal ATG codons.

Advantageously, the method according to the present invention may alsobe practiced using fragments of DNA or of a nucleic acid sequence. Theterm “DNA fragment or DNA segment” refers to a piece of DNA derived orprepared from an original (larger) DNA molecule. The term is notrestrictive to the content of the DNA fragment or segment. For example,the DNA fragment or segments can comprise many genes, with or withoutadditional control elements or may contain spacer sequences. Afunctional fragment refers to a piece of DNA derived or prepared from anoriginal (larger) DNA molecule, which DNA portion, when introduced andexpressed in a plant, gives plants having altered characteristics. Thefragments may be made by making one or more deletions and/or truncationsto the nucleic acid sequence. Techniques for introducing truncations anddeletions into a nucleic acid are well known in the art.

Another example of variants useful in the methods of the presentinvention, encompasses nucleic acid sequences capable of hybridisingwith a nucleic acid sequence as presented in any one of SEQ ID NO 1 to2755 or a nucleic acid encoding a protein as presented in any one of SEQID NO 1 to 2755.

The term “hybridisation” as defined herein is the process whereinsubstantially homologous complementary nucleotide sequences anneal toeach other. The hybridisation process can occur entirely in solution,i.e. both complementary nucleic acids are in solution. Tools inmolecular biology relying on such a process include the polymerase chainreaction (PCR; and all methods based thereon), subtractivehybridisation, random primer extension, nuclease S1 mapping, primerextension, reverse transcription, cDNA synthesis, differential displayof RNAs, and DNA sequence determination. The hybridisation process canalso occur with one of the complementary nucleic acids immobilised to amatrix such as magnetic beads, Sepharose beads or any other resin. Toolsin molecular biology relying on such a process include the isolation ofpoly (A+) mRNA. The hybridisation process can furthermore occur with oneof the complementary nucleic acids immobilised to a solid support suchas a nitro-cellulose or nylon membrane or immobilised by e.g.photolithography to e.g. a siliceous glass support (the latter known asnucleic acid arrays or microarrays or as nucleic acid chips). Tools inmolecular biology relying on such a process include RNA and DNA gel blotanalysis, colony hybridisation, plaque hybridisation, in situhybridisation and microarray hybridisation. In order to allowhybridisation to occur, the nucleic acid molecules are generallythermally or chemically denatured to melt a double strand into twosingle strands and/or to remove hairpins or other secondary structuresfrom single stranded nucleic acids. The stringency of hybridisation isinfluenced by conditions such as temperature, salt concentration andhybridisation buffer composition. High stringency conditions forhybridisation include high temperature and/or low salt concentration(salts include NaCl and Na₃-citrate) and/or the inclusion of formamidein the hybridisation buffer and/or lowering the concentration ofcompounds such as SDS (detergent) in the hybridisation buffer and/orexclusion of compounds such as dextran sulphate or polyethylene glycol(promoting molecular crowding) from the hybridisation buffer.Conventional hybridisation conditions are described in, for example,Sambrook (2001), but the skilled craftsman will appreciate that numerousdifferent hybridisation conditions can be designed in function of theknown or the expected homology and/or length of the nucleic acidsequence. With specifically hybridising is meant hybridising understringent conditions. Specific conditions for “specifically hybridising”are for example: hybridising under stringent conditions such as atemperature of 60° C. followed by washes in 2×SSC, 0.1×SDS, and 1×SSC,0.1×SDS. Depending on the source and concentration of the nucleic acidinvolved in the hybridisation, alternative conditions of stringency maybe employed, such as medium stringency conditions. Examples of mediumstringency conditions include 1-4×SSC/0.25% w/v SDS at ≧45° C. for 2-3hours. Sufficiently low stringency hybridisation conditions areparticularly preferred to isolate nucleic acids heterologous to the DNAsequences of the invention defined supra. Elements contributing toheterology include allelism, degeneration of the genetic code anddifferences in preferred codon usage. The stringency conditions maystart low and be progressively increased until there is provided ahybridising nucleic acid, as defined hereinabove. Elements contributingto heterology include allelism, degeneration of the genetic code anddifferences in preferred codon usage.

Another variant useful in the methods for altering growthcharacteristics encompasses a nucleic acid sequence which is analternative splice variant of a gene of the present invention (depositedin the MIPS database under the accession numbers as presented in Tables1, 2, 4 or 5). The term “alternative splice variant” as used hereinencompasses variants in which introns and selected exons have beenexcised, replaced or added. Such splice variants may be found in natureor can be manmade. For example, introns or exons can be excised,replaced or added such that the mRNA has altered expression (e.g.seed-preferred expression), or altered response to specific signals).Preferred variants will be ones in which the biological activity of theproteins of the present invention remains unaffected, which can beachieved by selectively retaining functional segments of the proteins.Methods for making such splice variants are well known in the art.

Another example of a variant useful to alter plant characteristics, isan allelic variant of a gene essentially similar to any one of SEQ ID NO1 to 2755. Allelic variants exist in nature and encompassed within themethods of the present invention is the use of these isolated naturalalleles in the methods according to the invention. Allelic variantsencompass Single Nucleotide Polymorphisms (SNPs), as well as SmallInsertion/Deletion Polymorphisms (INDELs). The size of INDELs is usuallyless than 100 bp. SNPs and INDELs form the largest set of sequencevariants in naturally occurring polymorphic strains of most organisms.Allellic variation can also be created artificially, such as for exampleby the techniques of EMS mutagenesis. Typically such variants arecreated with the purpose of breeding the altered plant characteristicaccording to the present invention in a plant. Alternatively, naturallymutated alleles are the subject of such selection and breedingprogrammes, wherein the allele capable of conferring altered plantcharacteristics to the plant are selected and plants containing suchallele are used for further breeding the trait.

Accordingly, the present invention provides a method for altering plantcharacteristics, using a splice variant or an allelic variant of anucleic acid sequence according to any one of SEQ ID NO 1 to 2755.

The term “plant characteristic” means any characteristic of a plant,plant cell or plant tissue described hereafter. These characteristicsencompass but are not limited to, characteristics of plant development,plant growth, yield, biomass production, plant architecture, plantbiochemistry, plant physiology, metabolism, survival capacity, stresstolerance and more. DNA synthesis, DNA modification, endoreduplication,cell cycle, cell wall biogenesis, transcription regulation, signaltransduction, storage lipid mobilization, photosynthesis and more.

The term “altering plant characteristics” as used herein encompasses anychange in said characteristic such as increase, decrease or change intime or place. According to a preferred embodiment of the invention,altering a plant characteristics encompasses improving the plantcharacteristic, such as for example increasing the plant characteristic(e.g. yield), or accelerating the characteristic (e.g. growth rate).

“Growth” refers to the capacity of the plant or of plant parts to expandand increase in biomass. Altered growth refers amongst others to alteredgrowth rate, cycling time, the size, expansion or increase of the plant.Additionally and/or alternatively, growth characteristics may refer tocellular processes comprising, but not limited to, cell cycle (entry,progression, exit), cell division, cell wall biogenesis and/or DNAsynthesis, DNA modification and/or endoreduplication.

“Yield” refers to the harvestable part of the plant. “Biomass” refers toany part of the plants. These terms also encompass an increase in seedyield, which includes an increase in the biomass of the seed (seedweight) and/or an increase in the number of (filled) seeds and/or in thesize of the seeds and/or an increase in seed volume, each relative tocorresponding wild-type plants. An increase in seed size and/or volumemay also influence the composition of seeds. An increase in seed yieldcould be due to an increase in the number and/or size of flowers. Anincrease in yield may also increase the harvest index, which isexpressed as a ratio of the total biomass over the yield of harvestableparts, such as seeds.

“Plant development” means any cellular process of a plant that isinvolved in determining the developmental fate of a plant cell, inparticular the specific tissue or organ type into which a progenitorcell will develop. Typical plant characteristics according to thepresent invention are therefore characteristics relating to cellularprocesses relevant to plant development such as for example,morphogenesis, photomorphogenesis, shoot development, root development,vegetative development, reproductive development, stem elongation,flowering, regulatory mechanisms involved in determining cell fate,pattern formation, differentiation, senescence, time of flowering and/ortime to flower.

“Plant architecture”, as used herein refers to the external appearanceof a plant, including any one or more structural features or acombination of structural features thereof. Such structural featuresinclude the shape, size, number, position, colour, texture, arrangement,and patternation of any cell, tissue or organ or groups of cells,tissues or organs of a plant, including the root, stem, leaf, shoot,petiole, trichome, flower, petal, stigma, style, stamen, pollen, ovule,seed, embryo, endosperm, seed coat, aleurone, fibre, fruit, cambium,wood, heartwood, parenchyma, aerenchyma, sieve element, phloem orvascular tissue, amongst others.

The term “stress tolerance” is understood as the capability of bettersurvival and/or better performing in stress conditions such asenvironmental stress, which can be biotic or abiotic. Salinity, drought,heat, chilling and freezing are all described as examples of conditionswhich induce osmotic stress. The term “environmental stress” as used inthe present invention refers to any adverse effect on metabolism, growthor viability of the cell, tissue, seed, organ or whole plant which isproduced by a non-living or non-biological environmental stressor. Moreparticularly, it also encompasses environmental factors such as waterstress (flooding, water logging, drought, dehydration), anaerobic (lowlevel of oxygen, CO2 etc.), aerobic stress, osmotic stress, salt stress,temperature stress (hot/heat, cold, freezing, frost) or nutrientsdeprivation, pollutants stress (heavy metals, toxic chemicals), ozone,high light, pathogen (including viruses, bacteria, fungi, insects andnematodes) and combinations of these. Biotic stress is stress as aresult of the impact of a living organism on the plant. Examples arestresses caused by pathogens (virus, bacteria, nematodes insects etc.).Another example is stress caused by an organism, which is notnecessarily harmful to the plant, such as the stress caused by asymbiotic or an epiphyte. Accordingly, particular plant characteristicsaccording to the present invention encompass early vigour, survivalrate, stress tolerance.

Field-grown plants almost always experience some form of stress, albeitmild, and therefore the terms “growth”, “yield” “biomass production” or“biomass” do not distinguish the performance of plants undernon-stressed from performance under stress conditions. Advantageously,the effects of the invention on growth and yield are expected to occurunder both severe and mild stress conditions (i.e. under stressed andnon-stressed conditions).

Characteristics related to “plant physiology” encompass characteristicsof functional processes of a plant, including developmental processessuch as growth, expansion and differentiation, sexual development,sexual reproduction, seed set, seed development, grain filling, asexualreproduction, cell division, dormancy, germination, light adaptation,photosynthesis, leaf expansion, fiber production, secondary growth orwood production, amongst others; responses of a plant toexternally-applied factors such as metals, chemicals, hormones, growthfactors, environment and environmental stress factors (e.g. anoxia,hypoxia, high temperature, low temperature, dehydration, light, daylength, flooding, salt, heavy metals, amongst others), includingadaptive responses of plants to said externally-applied factors.Particular plant physiology characteristics which are altered accordingto the methods of the present invention encompass altered storage lipidmobilization, photosynthesis, transcription regulation and signaltransduction.

Characteristics related to “plant biochemistry” are to be understood bythose skilled in the art to refer to the metabolic characteristics.“Metabolism” as used in the present invention is interchangeable withbiochemistry. Metabolism and/or biochemistry encompass catalytic orassimilation or other metabolic processes of a plant, including primaryand secondary metabolism and the products thereof, including anyelement, small molecules, macromolecules or chemical compounds, such asbut not limited to starches, sugars, proteins, peptides, enzymes,hormones, growth factors, nucleic acid molecules, celluloses,hemicelluloses, calloses, lectins, fibres, pigments such asanthocyanins, vitamins, minerals, micronutrients, or macronutrients,that are produced by plants. Preferably, the methods of the presentinvention are used to change the nitrogen or carbon metabolism.

As shown in Tables 1 and 2, several of the E2Fa-DPa target genesidentified have an E2F recognition sequence in their promoter and mostof these genes are involved in DNA replication. Therefore, provided by aparticular embodiment of the present invention is a method as describedabove to influence DNA synthesis and DNA replication. The secondaryinduced genes, which are the genes not having the E2F target consensussequence in their promoter region, encode proteins involved in cell wallbiosynthesis, transcription, signal transduction, or have an unknownfunction. Surprisingly, a large number of metabolic genes were modifiedas well, mainly genes involved in nitrate assimilation or metabolism andcarbon metabolism.

The putative direct E2Fa-DPa target genes as identified by the presenceof an E2F-DP-binding site, mainly belong to the group of genes involvedin DNA synthesis, whereas the secondary induced genes are mainly linkedto nitrogen assimilation and carbohydrate metabolism. Therefore, it iselucidated by the present invention that enhanced levels of E2Fa-DPa inplants have an impact on expression levels of genes involved in nitrogenassimilation and/or carbon metabolism. The experimental data suggestthat in E2Fa/DPa overexpressing plants there is a drain of nitrogen tothe nucleotide synthesis pathway causing a decreased synthesis of othernitrogen compounds such as amino acids and storage proteins.Corresponding to these findings, the inventors found that the level ofendoreduplication of E2Fa-DPa transgenic plants depends on the amount ofnitrogen available in the medium. Also, these data suggest that thegrowth arrest observed upon E2Fa/DPa expression results at least from anitrogen drain to the nucleotide synthesis pathway, causing a decreasedsynthesis of other nitrogen components, such as amino acids and storagecomponents.

As purine and pyrimidine bases are nitrogen-rich, the induction ofnitrogen assimilation genes in the E2Fa-DPa transgenic plants is amechanism to supply enough nitrogen for nucleotide biosynthesis. Mostlikely this drain of nitrogen from essential biosynthetic pathways tothe nucleotide biosynthesis pathway has its effects on many aspects ofplant metabolism, as can be seen from the reduction of expression ofvegetative storage protein genes and genes involved in amino-acidbiosynthesis.

Therefore a particular aspect of the invention is the use of genesinvolved in carbon and/or nitrogen metabolism or allocation, foraltering nitrogen and carbon metabolism and/or to alter the balancebetween carbon and nitrogen or to reallocate carbon and/or nitrogen orto alter the composition of components containing carbon and nitrogen.The elucidation of genes that are able to shift the nitrogenassimilation from one biological process to another biological processis important for many applications. These genes can for example be usedto alter the nitrogen composition of nitrogen-containing compounds in acell, such as nicotinamide-containing molecules, amino acid, nucleicacid, chlorophyll or any other metabolites. Also within the scope of thepresent inventions are these altered components obtainable by themethods of the present invention, with altered balance between carbonand nitrogen.

Therefore, according to the present invention, there is provided amethod as described above, wherein said altered metabolism comprisesaltered nitrogen and/or carbon metabolism.

In a particular embodiment, said carbon metabolism comprises theprocesses of carbon fixation, photosynthesis and photorespiration. Inanother embodiment, said nitrogen metabolism comprises nitrogen fixationor the reallocation of nitrogen residues from the pool of amino acidsinto the pool of nucleic acids or vice versa.

Microarray analysis of E2Fa-DPa overexpressing lines, as hereindescribed, identified a cross-talking matrix between DNA replication,nitrogen assimilation and photosynthesis. It has been describedpreviously that there is a link between carbon:nitrogen availability andgrowth, storage lipid mobilization and photosynthesis (Martin T.(2002)). Therefore according to the present invention there is provided,a method as described above, wherein said altered plant characteristiccomprises altered storage lipid mobilization and/or photosynthesis.

The microarray studies elucidated for the first time particular genesthat are upregulated and particular genes that are downregulated in aplant cell overexpressing E2Fa/DPa, many of which were of unknownfunction. It is now disclosed how to use these genes and/or proteins foraltering plant characteristics.

According to a preferred embodiment, recombinant means are used to alterplant characteristics. More preferably, one or more of the genesessentially similar to any of SEQ ID NO 1 to 2755 is introduced into aplant as a transgene. Accordingly, the present invention provides arecombinant nucleic acid comprising:

-   (a) one or more nucleic acid sequences essentially similar to any    one of SEQ ID NO 1 to 2755; optionally operably linked to-   (b) a regulatory sequence; and optionally operably linked to-   (c) a transcription termination sequence.

This recombinant nucleic acid is suitable for altering plant growthcharacteristics.

Constructs useful in the methods according to the present invention maybe constructed using recombinant DNA technology well known to personsskilled in the art. The gene constructs may be inserted into vectors,which may be commercially available, suitable for transforming intoplants and suitable for expression of the gene of interest in thetransformed cells.

The genetic construct can be an expression vector wherein said nucleicacid sequence is operably linked to one or more control sequencesallowing expression in prokaryotic and/or eukaryotic host cells.

The methods according to the present invention may also be practised byintroducing into a plant at least a part of a (natural or artificial)chromosome (such as a Bacterial Artificial Chromosome (BAC)), whichchromosome contains at least a gene/nucleic acid according to thepresent invention, optionally together with one or more related genefamily members or genes belonging to the same functional group as forexample the functional groups presented in Table 1 or 2. Therefore,according to a further aspect of the present invention, there isprovided a method to alter plant characteristics, comprisingintroduction into a plant at least a part of a chromosome comprising atleast a gene/nucleic, which gene/nucleic is essentially similar to anyone of SEQ ID NO 1 to 2755.

In a particular embodiment of the present invention said regulatorysequence is a plant-expressible promoter. In a further embodiment of theinvention the promoter is a constitutive promoter, such as the GOS2promoter, the ubiquitin promoter, the actin promoter. In anotherembodiment of the invention the promoter is a promoter active in themeristem or in dividing cells, such as, but not limited to the cdc2promoter, RNR promoter, MCM3 promoter. Alternatively, the regulatoryelement as mentioned above can be a translational enhancer, or atranscriptional enhancer that is used to enhance expression of a geneaccording to the present invention.

The term “Regulatory sequence” refers to control DNA sequences, whichare necessary to affect expression of coding sequences to which they areoperably linked. The nature of such control sequences differs dependingupon the host organism. In prokaryotes, control sequences generallyinclude promoters, ribosomal binding sites, and terminators. Ineukaryotes generally control sequences include promoters, terminatorsand enhancers or silencers. The term “control sequence” is intended toinclude, at a minimum, all components the presence of which arenecessary for expression, and may also include additional advantageouscomponents and which determines when, how much and where a specific geneis expressed. Reference herein to a “promoter” is to be taken in itsbroadest context and includes the transcriptional regulatory sequencesderived from a classical eukaryotic genomic gene, including the TATA boxwhich is required for accurate transcription initiation, with or withouta CCAAT box sequence and additional regulatory elements (i.e. upstreamactivating sequences, enhancers and silencers) which alter geneexpression in response to developmental and/or external stimuli, or in atissue-specific manner. The term “promoter” also includes thetranscriptional regulatory sequences of a classical prokaryotic gene, inwhich case it may include a −35 box sequence and/or a −10 boxtranscriptional regulatory sequences.

The term “promoter” is also used to describe a synthetic or fusionmolecule or derivative, which confers; activates or enhances expressionof a nucleic acid molecule in a cell, tissue or organ. “Promoter” is aDNA sequence generally described as the 5′-region of a gene, locatedproximal to the start codon. The transcription of an adjacent DNAsegment is initiated at the promoter region. In the context of thepresent invention, the promoter preferably is a plant-expressiblepromoter sequence. Promoters, however, that also function or solelyfunction in non-plant cells such as bacteria, yeast cells, insect cellsand animal cells are not excluded from the invention. By“plant-expressible” is meant that the promoter sequence, including anyadditional regulatory elements added thereto or contained therein, is atleast capable of inducing, conferring, activating or enhancingexpression in a plant cell, tissue or organ, preferably amonocotyledonous or dicotyledonous plant cell, tissue, or organ.

Preferably, the nucleic acid sequence capable of modulating expressionof a gene encoding an E2F target protein is operably linked to aconstitutive promoter or a tissue specific promoter. The term“constitutive” as defined herein refers to a promoter that is activepredominantly in at least one tissue or organ and predominantly at anylife stage of the plant. Preferably the promoter is active predominantlybut not exclusively throughout the plant

Additionally and/or alternatively, the nucleic acid of the presentinvention may be operably linked to a tissue-specific promoter. The term“tissue-specific” promoter as defined herein refers to a promoter thatis active predominantly but not exclusively in at least one tissue ororgan.

Examples of preferred promoters useful for the methods of the presentinvention are presented in Table I, II, III and IV. TABLE I Exemplaryconstitutive promoters for use in the performance of the presentinvention GENE EXPRESSION SOURCE PATTERN REFERENCE Actin constitutiveMcElroy et al, Plant Cell, 2: 163-171, 1990 CAMV constitutive Odell etal, Nature, 313: 810-812, 1985 35S CaMV constitutive Nilsson et al.,Physiol. Plant. 100: 19S 456-462, 1997 GOS2 constitutive de Pater et al,Plant J Nov; 2(6): 837-44, 1992 ubiquitin constitutive Christensen etal, Plant Mol. Biol. 18: 675-689, 1992 rice constitutive Buchholz et al,Plant Mol Biol. 25(5): cyclophilin 837-43, 1994 maize H3 constitutiveLepetit et al, Mol. Gen. Genet. 231: histone 276-285, 1992 actin 2constitutive An et al, Plant J. 10(1); 107-121, 1996

TABLE II Exemplary seed-preferred promoters for use in the performanceof the present invention EXPRESSION GENE SOURCE PATTERN REFERENCEseed-specific genes seed Simon, et al., Plant Mol. Biol. 5: 191, 1985;Scofield, et al., J. Biol. Chem. 262: 12202, 1987.; Baszczynski, et al.,Plant Mol. Biol. 14: 633, 1990. Brazil Nut albumin seed Pearson, et al.,Plant Mol. Biol. 18: 235-245, 1992. legumin seed Ellis, et al., PlantMol. Biol. 10: 203-214, 1988. glutelin (rice) seed Takaiwa, et al., Mol.Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221: 43-47,1987. zein seed Matzke et al Plant Mol Biol, 14(3): 323-32 1990 napAseed Stalberg, et al, Planta 199: 515-519, 1996. wheat LMW and HMWendosperm Mol Gen Genet 216: 81-90, 1989; NAR 17: 461-2, glutenin-1 1989wheat SPA seed Albani et al, Plant Cell, 9: 171-184, 1997 wheat a, b andg- endosperm EMBO 3: 1409-15, 1984 gliadins barley Itr1 promoterendosperm barley B1, C, D, endosperm Theor Appl Gen 98: 1253-62, 1999;Plant J 4: 343-55, hordein 1993; Mol Gen Genet 250: 750-60, 1996 barleyDOF endosperm Mena et al, The Plant Journal, 116(1): 53-62, 1998 blz2endosperm EP99106056.7 synthetic promoter endosperm Vicente-Carbajosa etal., Plant J. 13: 629-640, 1998. rice prolamin NRP33 endosperm Wu et al,Plant Cell Physiology 39(8) 885-889, 1998 rice-globulin Glb-1 endospermWu et al, Plant Cell Physiology 39(8) 885-889, 1998 rice OSH1 embryoSato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122, 1996 ricealpha-globulin endosperm Nakase et al. Plant Mol. Biol. 33: 513-522,1997 REB/OHP-1 rice ADP-glucose PP endosperm Trans Res 6: 157-68, 1997maize ESR gene endosperm Plant J 12: 235-46, 1997 family sorgumgamma-kafirin endosperm PMB 32: 1029-35, 1996 KNOX embryo Postma-Haarsmaet al, Plant Mol. Biol. 39: 257-71, 1999 rice oleosin embryo and Wu etat, J. Biochem., 123: 386, 1998 aleuron sunflower oleosin seed (embryoCummins, et al., Plant Mol. Biol. 19: 873-876, 1992 and dry seed)

TABLE III Exemplary flower-specific promoters for use in the performanceof the invention Gene Expression source pattern REFERENCE AtPRP4 flowershttp://salus.medium.edu/mmg/tierney/html chalene flowers Van der Meer,et al., Plant Mol. Biol. 15, synthase 95-109, 1990. (chsA) LAT52 antherTwell et al Mol. Gen Genet. 217: 240-245 (1989) apetala-3 flowers

TABLE IV Alternative rice promoters for use in the performance of theinvention PRO # gene expression PRO0001 Metallothionein Mte transferlayer of embryo + calli PRO0005 putative beta-amylase transfer layer ofembryo PRO0009 putative cellulose synthase weak in roots PRO0012 lipase(putative) PRO0014 transferase (putative) PRO0016 peptidyl prolylcis-trans isomerase (putative) PRO0019 unknown PRO0020 prp protein(putative) PRO0029 noduline (putative) PRO0058 proteinase inhibitorRgpi9 seed PRO0061 beta expansine EXPB9 weak in young flowers PRO0063structural protein young tissues + calli + embryo PRO0069 xylosidase(putative) PRO0075 prolamine 10 Kda strong in endosperm PRO0076 allergenRA2 strong in endosperm PRO0077 prolamine RP7 strong in endospermPRO0078 CBP80 PRO0079 starch branching enzyme I PRO0080Metallothioneine-like ML2 transfer layer of embryo + calli PRO0081putative caffeoyl-CoA 3-O-methyltransferase shoot PRO0087 prolamine RM9strong in endosperm PRO0090 prolamine RP6 strong endosperm PRO0091prolamine RP5 strong in endosperm PRO0092 allergen RA5 PRO0095 putativemethionine aminopeptidase embryo PRO0098 ras-related GTP binding proteinPRO0104 beta expansine EXPB1 PRO0105 Glycine rich protein PRO0108metallothionein like protein (putative) PRO0109 metallothioneine(putative) PRO0110 RCc3 strong root PRO0111 uclacyanin 3-like proteinweak discrimination center/ shoot meristem PRO0116 26S proteasomeregulatory particle non-ATPase very weak meristem specific subunit 11PRO0117 putative 40S ribosomal protein weak in endosperm PRO0122chlorophyll a/b-binding protein precursor (Cab27) very weak in shootPRO0123 putative protochlorophyllide reductase strong leaves PRO0126metallothionein RiCMT strong discrimination center/ shoot meristemPRO0129 GOS2 strong constitutive PRO0131 GOS9 PRO0133 chitinase Cht-3very weak meristem specific PRO0135 alpha-globulin strong in endospermPRO0136 alanine aminotransferase weak in endosperm PRO0138 cyclin A2PRO0139 Cyclin D2 PRO0140 Cyclin D3 PRO0141 cyclophyllin 2 shoot andseed PRO0146 sucrose synthase SS1 (barley) medium constitutive PRO0147trypsin inhibitor ITR1 (barley) weak in endosperm PRO0149 ubiquitine 2with intron strong constitutive PRO0151 WSI18 embryo + stress PRO0156HVA22 homologue (putative) PRO0157 EL2 PRO0169 aquaporine mediumconstitutive in young plants PRO0170 High mobility group protein strongconstitutive PRO0171 reversibly glycosylated protein RGP1 weakconstitutive PRO0173 cytosolic MDH shoot PRO0175 RAB21 embryo + stressPRO0176 CDPK7 PRO0177 Cdc2-1 very weak in meristem PRO0197 sucrosesynthase 3 PRO0198 OsVP1 PRO0200 OSH1 very weak in young plant meristemPRO0208 putative chlorophyllase PRO0210 OsNRT1 PRO0211 EXP3 PRO0216phosphate transporter OjPT1 PRO0218 oleosin 18 kd aleurone + embryoPRO0219 ubiquitine 2 without intron PRO0220 RFL PRO0221 maize UBI deltaintron not detected PRO0223 glutelin-1 PRO0224 fragment of prolamin RP6promoter PRO0225 4xABRE PRO0226 glutelin OSGLUA3 PRO0227 BLZ-2_short(barley) PRO0228 BLZ-2_long (barley)

Optionally, one or more terminator sequences may also be used in theconstruct introduced into a plant. The term “terminator” encompasses acontrol sequence which is a DNA sequence at the end of a transcriptionalunit which signals 3′ processing and polyadenylation of a primarytranscript and termination of transcription. Additional regulatoryelements may include transcriptional as well as translational enhancers.Those skilled in the art will be aware of terminator and enhancersequences, which may be suitable for use in performing the invention.Such sequences would be known or may readily be obtained by a personskilled in the art.

The genetic constructs of the invention may further include an origin ofreplication sequence which is required for maintenance and/orreplication in a specific cell type. One example is when a geneticconstruct is required to be maintained in a bacterial cell as anepisomal genetic element (e.g. plasmid or cosmid molecule). Preferredorigins of replication include, but are not limited to, the f1-ori andcolE1.

The genetic construct may optionally comprise a selectable marker gene.As used herein, the term “selectable marker gene” includes any gene,which confers a phenotype on a cell in which it is expressed tofacilitate the identification and/or selection of cells which aretransfected or transformed with a nucleic acid construct of theinvention. Suitable markers may be selected from markers that conferantibiotic or herbicide resistance, that introduce a new metabolic traitor that allow visual selection. Examples of selectable marker genesinclude genes conferring resistance to antibiotics (such as nptIIencoding neomycin phosphotransferase capable of phosphorylating neomycinand kanamycin, or hpt encoding hygromycin phosphotransferase capable ofphosphorylating hygromycin), to herbicides (for example bar whichprovides resistance to Basta; aroA or gox providing resistance againstglyphosate), or genes that provide a metabolic trait (such as manA thatallows plants to use mannose as sole carbon source). Visual marker genesresult in the formation of colour (for example beta-glucuronidase, GUS),luminescence (such as luciferase) or fluorescence (Green FluorescentProtein, GFP, and derivatives thereof. Further examples of suitableselectable marker genes include the ampicillin resistance (Ampr),tetracycline resistance gene (Tcr), bacterial kanamycin resistance gene(Kanr), phosphinothricin resistance gene, and the chloramphenicolacetyltransferase (CAT) gene, amongst others

The methods of the present invention are particularly relevant forapplications in agriculture and horticulture, and serve to developplants that have altered characteristics.

Accordingly, another embodiment of the invention is a method for makinga transgenic plant comprising the introduction of a recombinant nucleicacid as mentioned above into a plant. “A plant” as used herein meansplant cell, plant part etc. as defined herein below.

According to a preferred embodiment this method for the production of atransgenic plant further comprises the step of cultivating the plantcell under conditions promoting regeneration and mature plant growth.

A further embodiment relates to a method as described above, comprisingstably integrating into the genome of a plant a recombinant nucleic acidas mentioned above. Alternatively, the recombinant nucleic acidscomprising the nucleic acids of the present invention are transientlyintroduced into a plant or plant cell. The protein itself and/or thenucleic acid itself may be introduced directly into a plant cell or intothe plant itself (including introduction into a tissue, organ or anyother part of the plant). According to a preferred feature of thepresent invention, the nucleic acid is preferably introduced into aplant by transformation.

The term “transformation” as referred to herein encompasses the transferof an exogenous polynucleotide into a host cell, irrespective of themethod used for transfer. Plant tissue capable of subsequent clonalpropagation, whether by organogenesis or embryogenesis, may betransformed with a genetic construct of the present invention and awhole plant regenerated therefrom. The particular tissue chosen willvary depending on the clonal propagation systems available for, and bestsuited to, the particular species being transformed. Exemplary tissuetargets include leaf disks, pollen, embryos, cotyledons, hypocotyls,megagametophytes, callus tissue, existing meristematic tissue (e.g.,apical meristem, axillary buds, and root meristems), and inducedmeristem tissue (e.g. cotyledon meristem and hypocotyl meristem). Thepolynucleotide may be transiently or stably introduced into a host celland may be maintained non-integrated, for example, as a plasmid.Alternatively and preferably, the transgene may be stably integratedinto the host genome. The resulting transformed plant cell can then beused to regenerate a transformed plant in a manner known to personsskilled in the art.

Transformation of a plant species is now a fairly routine technique.Advantageously, any of several transformation methods may be used tointroduce the gene of interest into a suitable ancestor cell.Transformation methods include the use of liposomes, electroporation,chemicals that increase free DNA uptake, injection of the DNA directlyinto the plant, particle gun bombardment, transformation using virusesor pollen and microprojection. Methods may be selected from thecalcium/polyethylene glycol method for protoplasts (Krens et al., 1982;Negrutiu et al., 1987); electroporation of protoplasts (Shillito et al.,1985); microinjection into plant material (Crossway et al., 1986); DNAor RNA-coated particle bombardment (Klein et al., 1987) infection with(non-integrative) viruses and the like.

Transgenic rice plants expressing a gene according to the presentinvention are preferably produced via Agrobacterium-mediatedtransformation using any of the well known methods for ricetransformation, such as described in any of the following: publishedEuropean patent application EP 1198985 A1, Aldemita and Hodges (1996);Chan et al. (1993), Hiei et al. (1994), which disclosures areincorporated by reference herein as if fully set forth. In the case ofcorn transformation, the preferred method is as described in eitherIshida et al. (1996) or Frame et al. (2002), which disclosures areincorporated by reference herein as if fully set forth.

Generally after transformation, plant cells or cell groupings areselected for the presence of one or more markers which are encoded byplant-expressible genes co-transferred with the gene of interest,following which the transformed material is regenerated into a wholeplant.

Following DNA transfer and regeneration, putatively transformed plantsmay be evaluated, for instance using Southern analysis, for the presenceof the gene of interest, copy number and/or genomic organisation.Alternatively or additionally, expression levels of the newly introducedDNA may be monitored using Northern and/or Western analysis, bothtechniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety ofmeans, such as by clonal propagation or classical breeding techniques.For example, a first generation (or T1) transformed plant may be selfedto give homozygous second generation (or T2) transformants, and the T2plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. Forexample, they may be chimeras of transformed cells and non-transformedcells; clonal transformants (e.g., all cells transformed to contain theexpression cassette); grafts of transformed and untransformed tissues(e.g., in plants, a transformed rootstock grafted to an untransformedscion).

The present invention also encompasses plants obtainable by the methodsaccording to the present invention. The present invention providesplants having one or more altered characteristics, when compared to thewild-type plants, characterised in that the plant has modifiedexpression of one or more nucleic acids and/or modified level and/oractivity of a protein, wherein said nucleic acid and/or protein areessentially similar to any one of SEQ ID NO 1 to 2755.

In one embodiment of the present invention, such a plant is a transgenicplant. According to a further embodiment such transgenic plant comprisesan isolated nucleic acid and/or protein sequence essentially similar toany one for Seq Id NO 1 to 2755.

Alternatively, according to one embodiment of the present invention,such a plant having one or more altered plant characteristics and havingmodified expression of one or more nucleic acids and/or modified leveland/or activity of a protein, wherein said nucleic acid and/or proteinare essentially similar to any one of SEQ ID NO 1 to 2755, is created bybreeding techniques.

The present invention clearly extends to any plant cell or plantproduced by any of the methods described herein, and to all plant partsand propagules thereof. The present invention extends further toencompass the progeny of a primary transformed or transfected cell,tissue, organ or whole plant that has been produced by any of theaforementioned methods, the only requirement being that progeny exhibitthe same genotypic and/or phenotypic characteristic(s) as those producedin the parent by the methods according to the invention. The inventionaccordingly also includes host cells containing an isolated nucleic acidmolecule encoding a protein essentially similar to any one of SEQ ID NO1 to 2755. Such host cell may be selected from plants, bacteria,animals, algae, fungi, yeast or insects. Preferred host cells accordingto the invention are plant cells. The invention also extends toharvestable parts of a plant such as but not limited to seeds, leaves,fruits, flowers, stem cultures, stem, rhizomes, roots, tubers and bulbs.

The term “plant” as used herein encompasses whole plants, ancestors andprogeny of the plants and plant parts, including seeds, shoots, stems,roots (including tubers), and plant cells, tissues and organs. The term“plant” also therefore encompasses suspension cultures, embryos,meristematic regions, callus tissue, leaves, gametophytes, sporophytes,pollen, and microspores. Plants that are particularly useful in themethods of the invention include all plants which belong to thesuperfamily Viridiplantae, in particular monocotyledonous anddicotyledonous plants including a fodder or forage legume, ornamentalplant, food crop, tree, or shrub selected from the list comprisingAcacia spp., Acer spp., Actinidia spp., Aesculus spp., Agathisaustralis, Albizia amara, Alsophila tricolor, Andropogon spp., Arachisspp, Areca catechu, Astelia fragrans, Astragalus cicer, Baikiaeaplurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkeaafricana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camelliasinensis, Canna indica, Capsicum spp., Cassia spp., Centroema pubescens,Chaenomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermummopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumisspp., Cupressus spp., Cyathea dealbata, Cydonia oblonga, Cryptomeriajaponica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergiamonetaria, Davallia divaricata, Desmodium spp., Dicksonia squarosa,Diheteropogon amplectens, Dioclea spp, Dolichos spp., Dorycnium rectum,Echinochloa pyramidalis, Ehrartia spp., Eleusine coracana, Eragrestisspp., Erythrina spp., Eucalyptus spp., Euclea schimperi, Eulaliavillosa, Fagopyrum spp., Feijoa sellowiana, Fragaria spp., Flemingiaspp, Freycinetia banksii, Geranium thunbergii, Ginkgo biloba, Glycinejavanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtiacoleosperma, Hedysarum spp., Hemarthia alfussima, Heteropogon contortus,Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypertheliadissolute, Indigo incarnata, Iris spp., Leptarrhena pyrolifolia,Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex,Lotonus bainesii, Lotus spp., Macrotyloma axillare, Malus spp., Manihotesculenta, Medicago sativa, Metasequoia glyptostroboides, Musasapientum, Nicotianum spp., Onoblychis spp., Omithopus spp., Oryza spp.,Peltophorum africanum, Pennisetum spp., Persea gratissima, Petunia spp.,Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photinia spp.,Picea glauca, Pinus spp., Pisum sativum, Podocarpus totara, Pogonarthriafleckii, Pogonathria squarrosa, Populus spp., Prosopis cineraria,Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis, Quercusspp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhus natalensis,Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosa spp., Rubusspp., Salix spp., Schyzachyrium sanguineum, Sciadopitys verticillata,Sequoia sempervirens, Sequoiadendron giganteum, Sorghum bicolor,Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides,Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themedatriandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vacciniumspp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschiaaethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brusselssprouts, cabbage, canola, carrot, cauliflower, celery, collard greens,flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean,straw, sugar beet, sugar cane, sunflower, tomato, squash tea, trees.Alternatively algae and other non-Viridiplantae can be used for themethods of the present invention. Preferably the plant according to thepresent invention is a crop plant selected from rice, maize, wheat,barley, soybean, sunflower, canola, sugarcane, alfalfa, millet,leguminosae (bean, pea), flax, lupinus, rapeseed, tobacco, popular andcotton. Further preferably, the plant according to the present inventionis a monocotyledonous plant, most preferably a cereal.

The term ‘gene(s)’ or ‘nucleic acid’, ‘nucleotide sequence’, as usedherein refers to a polymeric form of a deoxyribonucleotides orribonucleotide polymer of any length, either double- or single-stranded,or analogs thereof, that have the essential characteristics of a naturalribonucleotide in that they can hybridize to nucleic acids in a mannersimilar to naturally occurring polynucleotides. A great variety ofmodifications have been made to DNA and RNA that serve many usefulpurposes known to those skilled in the art. For example, methylation,‘caps’ and substitution of one or more of the naturally occurringnucleotides with an analog. Said terms also include peptide nucleicacids. The term “polynucleotide” as used herein includes suchchemically, enzymatyically or metabolically modified forms ofpolynucleotides.

With “recombinant nucleic acid” is meant a nucleic acid produced byjoining pieces of DNA from different sources through deliberate humanmanipulation.

The inventors identified genes that are upregulated in plantsoverexpressing E2Fa/DPa. These genes can be used to simulate E2Fa/DParelated effect in a plant.

Therefore, according to the invention, there is provided a method toalter characteristics of a plant, comprising overexpression of one ormore nucleic acids essentially similar to any one of SEQ ID NO 1 to2755, or wherein the method comprises enhancing the level and/oractivity of one or more proteins essentially similar to a proteinsequence essentially similar to any one of SEQ ID NO 1 to 2755.

Also identified were genes that are downregulated in plantsoverexpressing E2Fa/DPa. These genes can be used to simulate E2Fa/DParelated effect in a plant. Therefore, according to the invention, thereis provided a method to alter plant growth characteristics, comprisingdownregulation of expression of one or more nucleic acids essentiallysimilar to any one of SEQ ID NO 1 to 2755, or wherein the methodcomprises decreasing level and/or activity of one or more proteinsessentially similar to any one of SEQ ID NO 1 to 2755.

Genetic constructs aimed at silencing gene expression may comprise thenucleotide sequence essentially similar to any one of SEQ ID NO 1 to2755 or one at least a portion thereof in a sense and/or antisenseorientation relative to the promoter sequence. Preferably the portionscomprises at least 21 contiguous nucleic acid of a sequence to bedownregulated. Also, sense or antisense copies of at least part of theendogenous gene in the form of direct or inverted repeats may beutilized in the methods according to the invention. The characteristicsof plants may also be changed by introducing into a plant at least partof an antisense version of the nucleotide sequence essentially similarto any one or more of SEQ ID NO 1 to 2755. It should be clear that partof the nucleic acid (a portion) could also achieve the desired result.Homologous anti-sense genes are preferred, homologous genes being plantgenes, preferably plant genes from the same plant species in which thesilencing construct is introduced.

Detailed analysis of the promoters of the genes identified in thepresent invention allowed the identification of novel E2Fa/DPa targetgenes that are under the direct control of E2Fa/DPa and that are mainlyinvolved in DNA replication. For all the genes identified in the presentinvention, reference is made to the MIPS database MATDB accessionnumber. This unique identification number refers to the deposit ofinformation related to the gene in question, e.g. the unsplicedsequence, the spliced sequence, the protein sequence, the domains of theprotein etc. An example of the information deposited under the accessionnumber At1g57680 is shown in FIG. 4. Based on this unique accessionnumber, a person skilled in the art would be able to locate the geneprovided by the present invention in its genomic environment. From thisinformation one can identify and isolate the upstream control elementsof these genes. Especially interesting are the promoters of these genesas control elements for driving or regulating transcription ofheterologous genes. Therefore, according to the invention is provided anisolated nucleic acid comprising one or more of the regulatory elementsupstream of the start codon of the nucleic acids essentially similar toany one of SEQ ID NO 1 to 2755. Furthermore, the invention provides anisolated nucleic acid as mentioned above, wherein said regulatoryelement is the promoter of said the genes essentially similar to any oneof the sequence presented in SEQ ID NO 1 to 2755.

Further the invention also relates to the use of a nucleic acid sequenceor protein essentially similar to any one of SEQ ID NO 1 to 2755, foraltering plant characteristics.

Another method for altering plant characteristics and/or growthcharacteristics of a plant resides in the use of allelic variants of thegenes of the present invention. Allelic variants exist in nature andencompassed within the methods of the present invention is the use ofthese natural alleles. Alternatively, in particular breeding programs,such as for example marker assisted breeding, or conventional breedingprogrammes, it is sometimes practical to introduce allelic variation inthe plants by mutagenic treatment of a plant. One suitable mutagenicmethod is EMS mutagenesis. Identification of allelic variants then takesplace by, for example, PCR. This is followed by a selection step forselection of superior allelic variants of the sequence in question andwhich give rise to altered growth characteristics. Selection istypically carried out by monitoring growth performance of plantscontaining different allelic variants of the sequence in question.Monitoring growth performance can be done in a greenhouse or in thefield. Further optional steps include crossing plants in which thesuperior allelic variant was identified with another plant. This couldbe used, for example, to make a combination of interesting phenotypicfeatures.

According to another aspect of the present invention, advantage may betaken of the nucleic acid sequence of the present invention in breedingprograms. In such a program, a DNA marker may be identified which isgenetically linked to the nucleic acid of the present invention. ThisDNA marker is then used in breeding programs to select plants havingaltered growth characteristics. Therefore, the present invention alsoencompass the use of a nucleic acid sequence essentially similar to anyone of SEQ ID NO 1 to 2755, for marker assisted breeding of plants withaltered characteristics.

These marker assisted breeding processes may further involve the stepsof crossing plants and using probes or primers having part, for examplehaving at least 10 bp, of a sequence corresponding to any of SEQ ID NO 1to 2755, to detect the DNA sequence corresponding to SEQ ID NO 1 to2755, in the progeny of the cross.

These methods for marker assisted breeding also may involve the use ofan isolated DNA molecule being essentially similar to SEQ ID NO 1 to2755 or a part thereof as a marker in techniques like AFLP, RFLP, RAPD,or in the detection of Single Nucleotide Polymorphisms.

Further these methods for marker assisted breeding also may involvedetermining the presence or absence in a plant genome of a qualitativetrait or a quantitative trait locus (QTL) linked to a transgeneessentially similar to any one of SEQ ID NO 1 to 2755 or to anendogenous homologue of any one of SEQ ID NO 1 to 2755, which methodcomprises:

-   (a) detecting a molecular marker linked to a QTL, wherein the    molecular marker comprises a sequence essentially similar to SEQ ID    NO 1 to 2755 or an endogenous homologue thereof; and-   (b) determining the presence of said QTL as by detection of the    molecular marker of step (a) or determining the absence of said QTL    as failure to detect the molecular marker of step (a)

Alternatively, methods for marker assisted breeding may involvedetecting the presence of a quantitative trait locus linked to a DNAsequence essentially similar to SEQ ID NO 1 to 2755 or to an endogenoushomologue thereof in the genome of a plant. The methods described abovemay involve the steps of:

-   (a) extracting a DNA sample of said plant;-   (b) contacting the DNA sample with a probe that hybridises to a DNA    sequence according to claim 1 or to an endogenous homologue thereof,    or to the complement thereof;-   (c) performing a hybridisation reaction under conditions suitable    for hybridisation of the probe to the DNA sample of (b); and-   (d) detecting the hybridisation of the probe to the DNA.

Further, the present invention also encompass the use of a nucleic acidsequence essentially similar to any one of SEQ ID NO 1 to 2755, forconventional breeding of plants with altered characteristics.

In conventional breeding programs, the nucleic acid essentially similarto any one of SEQ ID NO 1 to 2755 is used to select plants with betterplant characteristics compared to the normal wild-type plants. Theplants with better growth characteristics may originated from naturalvariation in the alleles of the gene corresponding to any one of SEQ IDNO 1 to 2755, or may originated from manmade variation in these genes,for example variation created by EMS mutagenesis or other methods tocreated single nucleotide polymorfisms.

Further the invention also relates to the use of a nucleic acid or aprotein essentially similar any one of SEQ ID NO 1 to 2755, as a growthregulator.

In a particular embodiment such a growth regulator is a herbicide or isa growth stimulator. The present invention therefore also provides agrowth regulating composition comprising a nucleic acid and/or a proteinessentially similar to any one of SEQ ID NO 1 to 2755. The growthregulating compositions according to the present invention canadditionally comprise any additive usually present in growth regulatingcompositions such as growth inhibitors, herbicides or growthstimulators. Also a kit comprising a sequence essentially similar to anyone of SEQ ID NO 1 to 2755 (for example in the form of a herbicide) isin the scope of the present invention. Also any other plant effectiveagent comprising the sequences according to the present invention areprovided herein. Methods to produce the compositions, kits or plantagents as mentioned above are also provided by the present invention andinvolve the production of any one or more of the sequences essentiallysimilar to any one of SEQ ID NO 1 to 2755. Such sequences and methodsare herein provided.

Further, plants of the present invention have improved characteristics,such as improved growth and yield, which makes these plant suitable toproduce industrial proteins.

Accordingly, the present invention provides a method for the productionof enzymes and/or pharmaceuticals, which method comprises modifyingexpression of a nucleic acid, and/or modifying level and/or activity ofa protein, said nucleic acid and/or protein being essentially similar toany one of SEQ ID NO 1 to 2755

The present invention therefore also encompasses the use of plants asdescribed above, for the production of (industrial) enzymes and/orpharmaceuticals. The (Industrial) enzymes and pharmaceuticals producedaccording to the method as described above are also encompasses by thepresent invention.

Also the invention as presented herein offers means to alter thecharacteristics not only of plants, but also of other organisms, such asmammals. The plant genes of the present invention, or their homologues,or the plant proteins or their homologues, can be used as therapeuticsor can be used to develop therapeutics for both humans and animals.Accordingly, the present invention relates to a nucleic acid or aprotein essentially similar to any one of SEQ ID NO 1 to 2755, for useas a therapeutic agent.

In a particular embodiment, the use as a therapeutic agents encompassesthe use in gene therapy, or the use to manufacture medicaments such asfor example therapeutic protein samples. Also the nucleic acids and/orproteins according to the present invention can be applied in diagnosticmethods.

Accordingly provided by the present invention is the use of a nucleicacid or a protein essentially similar to any one of SEQ ID NO 1 to 2755,for use as a therapeutic agent, a diagnostic means, a kit or planteffective agent.

Further encompassed by the invention are therapeutic or diagnosticcompositions or kits or plant effective agent, comprising a nucleic acidand/or a protein essentially similar to any one of SEQ ID NO 1 to 2755.These compositions may comprise other additives usually applied fortherapeutic compositions. Methods to produce these therapeutic ordiagnostic compositions or kts are also provided by the presentinvention and involve the production of any of the sequences essentiallysimilar to any one of SEQ ID NO 1 to 2755.

The plants according to the present invention have alteredcharacteristics, such as for example improved growth and yield, whichmakes them suitable sources for many agricultural applications and thefood industry. Accordingly, provided by the present invention there is afood product derived from a plant or host cell as described above andalso the use of such a food product in animal feed or food.

In molecular biology it is standard practice to select upon transfectionor transformation those individuals (or groups of individuals, such asbacterial or yeast colonies or phage plaques or eukaryotic cell clones)that are effectively transfected or transformed with the desired geneticconstruct. Typically these selection procedures are based on thepresence of a selectable or screenable marker in the transfected geneticconstruct, to distinguish the positive individuals easily from thenegative individuals. The nucleic acids and proteins according to thepresent invention are capable of altering the characteristics of thehost cells to which they are applied. Therefore, the nucleic acidsand/or proteins according to the present invention can also be used asselectable markers, screenable markers or selection agents. According toone particular embodiment, the present invention provides the use of anucleic acid or a protein essentially similar to any one of SEQ ID NO 1to 2755 as a positive or negative selectable marker duringtransformation of plant cell, plant tissue or plant procedures.

DESCRIPTION OF THE FIGURES

FIG. 1: Volcano plot of significance against effect. Each x representone of the 4579 genes, with the negative log10 of the P value from thegene model plotted against the difference between least-square means forthe genotype effect. The horizontal line represents the test-wisethreshold of P=0.05. The two vertical reference lines indicate a 2-foldcutoff for either repression or induction.

FIG. 2: Sources of alpha-ketoglutarate and other metabolites in plants,with annotation of up and downregulated genes in the E2Fa-DPaoverproducing cells. Upregulated enzymes are underlined with a dashedline and enzymes underlined with a full line are downregulated in theE2Fa-DPa versus wild type plants. Products that are boxed act asprecursors for nucleotide biosynthesis. A-KG, alpha-ketoglutarate;GOGAT, glutamate synthetase; NIA2, nitrate reductase, NiR, nitritereductase.

FIG. 3: Endoreduplication levels in wild type and E2Fa/DPa transgeniclines in relation to nitrogen availability. Wild type (A) and transgenic(B) lines were grown on minimal medium in the presence of 0.1, 1, 10, or50 mM ammonium nitrate. Values are means of three independentmeasurements.

FIG. 4: Represents the information which is deposited in the MatDB (MIPSArabidopsis database) under accession number At1g57680

FIG. 5: Verification of microarray analysis by RT-PCR. RT-PCR analysiswas carried out under linear amplification conditions. The actin 2 gene(ACT2) was used as loading control. GS, glutamine synthetase; GOGAT,glutamate synthase; NiR, nitrite reductase.

FIG. 6: NMR spectrum of E2Fa/DPa overexpressing plant cells.

Table 1: Presentation of Arabidopsis genes that are 2 fold or moreupregulated in E2Fa-DPa overexpressing plants. The genes are presentedaccording to the functional category to which they belong. For some ofthe genes, no function has been described in the public databases andthey are named unknown, putative or hypothetical protein. All the geneshave each a unique MIPS accession number, which refers to theidentification of the sequence in the MatDB (MIPS Arabidopsis thalianadatabase). The MIPS accession number refers to the protein entry codefor the MatDB of MIPS. Also, there is an accession number provided as aninternal protein code. The fold of induction is also given for eachsequence. Furthermore, where an E2F target sequence has been identifiedin the upstream region of the gene, the sequence of that site is alsopresented in the Table. Finally, other plant homologues which havesubstantial sequence identity with the Arabidopsis gene are mentioned inthis Table.

Table 2: Presentation of Arabidopsis genes that are 2 fold or morerepressed in E2Fa-DPa overexpressing plants. Data are presented in asimilar way as for Table 1, as explained above.

Table 3: Different E2F target sequences and the frequency of theirpresence in the upstream regions of the Arabidopsis genes described inthe present invention.

Table 4: Selection of the Arabidopsis genes from the microarray thatwere 1.3 times upregulated in E2Fa/DPa overexpressing plants, comparedto the wild-type plants. The gene name is given, as well as the MIPSdatabase accession number and a ratio indicating the degree ofupregulation of the gene. Furthermore, the E-value indicates if asignificant homologue has been found in the public databases.

Table 5: Selection of the Arabidopsis genes from the microarray thatwere 1.3 times repressed in E2Fa/DPa overexpressing plants, compared tothe wild-type plants. The data are presented as in Table 4. The foldrepression is calculated as 1/ratio. In this Table only the genes thathave a ratio of less than 0.77 are selected.

Table 6: genes selected for Arabidopsis transformation

Table 7: genes selected for rice transformation

EXAMPLES Example 1 Overexpression of E2Fa and DPa in Arabidopsis

Double transgenic CaMV35S-E2Fa-DPa overexpressing plants were obtainedby the crossing of homozygous CaMV35S-E2Fa and CaMV35S-DPa plants (DeVeylder et al., 2002). Double transformants were grown under a 16 hlight/8 h dark photoperiod at 22° C. on germination medium (Valvekens etal., 1988).

Selection of Transgenic Lines

Arabidopsis thaliana plants were generated that contained either theE2Fa or the DPa gene under the control of the constitutive cauliflowermosaic virus (CaMV) 35S promoter.

Crossing Experiments of Overexpressing E2Fa and DPa Lines

Plants homozygous for the CaMV 35S E2Fa gene were crossed withheterozygous CaMV 35S DPa lines. Polymerase chain reaction (PCR)analysis on individual plants confirmed which plants contained both theCaMV 35S-E2Fa and CaMV 35S-DPa constructs.

8 days after sowing, these plants were used to isolate total RNA, fromwhich cDNA was synthesized and subsequently hybridized to a microarraycontaining 4579 unique Arabidopsis ESTs. These experimental steps aredescribed in the following examples.

Example 2 Construction of Microarrays

Construction of Microarrays

The Arabidopsis thaliana microarray consisted of 4,608 cDNA fragmentsspotted in duplicate, distant from each other, on Type V silane coatedslides (Amersham BioSciences, Buckinghamshire, UK). The clone setincluded 4,579 Arabidopsis genes composed from the unigen clonecollection from Incyte (Arabidopsis Gem I, Incyte, USA). To retrieve thefunctional annotation of the genes relating to the spotted ESTs, BLASTNagainst genomic sequences was performed. To make the analysis easier acollection of genomic sequences bearing only one gene was builtaccording to the available annotations. Each of those sequences had itsupstream intergenic sequence followed by the exon-intron structure ofthe gene and the downstream intergenic sequence, intergenic being thewhole genomic sequence between start and stop codons from neighboringprotein-encoding genes. From the BLASTN output the best hits wereextracted and submitted to a BLASTX search against protein databases. Toretrieve even more detailed information concerning the potentialfunction of the genes, protein domains were searched using ProDom. Thecomplete data set can be found on the websitehttp://www.psb.rug.ac.be/E2F and is cited herein by reference. The cDNAinserts were PCR amplified using M13 primers, purified withMultiScreen-PCR plate (cat: MANU03050, Millipore, Belgium) and arrayedon the slides using a Molecular Dynamics Generation III printer(Amersham BioSciences). Slides were blocked in 3.5% SSC, 0.2% SDS, 1%BSA for 10 minutes at 60° C.

RNA Amplification and Labeling

Antisense RNA amplification was performed using a modified protocol ofin vitro transcription as described earlier in Puskas et al. (2002). Forthe first strand cDNA synthesis, 5 μg of total RNA was mixed with 2 μgof an HPLC-purified anchored oligo-dT+T7 promoter(5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-T₂₄(A/C/G)-3′) (SEQ ID NO2756). (Eurogentec, Belgium), 40 units of RNAseOUT (cat# 10777-019,Invitrogen, Merelbeke, Belgium) and 0.9M D(+) trehalose (cat# T-5251,Sigma Belgium) in a total volume of 11 μl, and heated to 75° C. for 5minutes. To this mixture, 4 μl 5× first strand buffer (Invitrogen,Belgium), 2 l 0.1 M DTT, 1 μl 10 mM dNTP mix, 1 μl 1.7 M D(+)trehalose(cat# T-5251, Sigma Belgium) and 1 μl, 200 Units of SuperScript II(cat#: 18064-014, Invitrogen, Belgium) was added in 20 μl final volume.The sample was incubated in a Biometra-Unoll thermocycler at 37° C. for5 minutes, 45° C. for 10 minutes, 10 cycles at 60° C. for 2 minutes andat 55° C. for 2 minutes. To the first strand reaction mix, 103.8 μlwater, 33.4 μl 5× second strand synthesis buffer (Invitrogen, Belgium),3.4 μl 10 mM dNTP mix, 1 μl of 10 U/μl E. coli DNA ligase (cat#:18052-019, Invitrogen, Belgium), 4 μl 10 U/μl E. coli DNA Polymerase I(cat#: 18010-025, Invitrogen, Belgium) and 1 μl 2 U/μl E. coli RNAse H(cat#: 18021-071, Invitrogen, Belgium) was added, and incubated at 16°C. for 2 hours. The synthesized double-stranded cDNA was purified withQiaquick (cat#: 28106, Qiagen, Hilden, Germany). Antisense RNA synthesiswas done by AmpliScribe T7 high yield transcription kit (cat#: AS2607;Epicentre Technologies, USA) in total volume of 20 μl according to themanufacturer's instructions. The RNA was purified with RNeasypurification kit (cat#: 74106; Qiagen, Germany). From this aRNA, 5 μgwas labeled by reverse transcription using random nonamer primers(Genset, Paris, France), 0.1 mM d(G/T/A)TPs, 0.05 mM dCTP (AmershamBioSciences, UK), 0.05 mM Cy3-dCTP or Cy5-dCTP (cat#: PA53023, PA55023;Amersham BioSciences, UK) 1× first strand buffer, 10 mM DTT and 200Units of SuperScript II (cat#: 18064-014, Invitrogen, Belgium) in 20 μltotal volume. The RNA and primers were denatured at 75° C. for 5 minutesand cooled on ice before adding the remaining reaction components. After2 hours incubation at 42° C., mRNA was hydrolyzed in 250 mM NaOH for 15minutes at 37° C. The sample was neutralized with 10 μl of 2 M MOPS andpurified with Qiaquick (cat#: 28106, Qiagen, Germany).

Array Hybridization and Post-Hybridization Processes

The probes were resuspended in 30 μl hybridization solution (50%formamide, 5×SSC, 0.1% SDS, 100 mg/ml salmon sperm DNA) andprehybridized with 1 μl poly-dT (1 mg/ml) at 42° C. for 30 minutes toblock hybridization on the polyA/T tails of the cDNA on the arrays. 1mg/ml mouse COT DNA (cat#: 18440-016, Invitrogen, Belgium) was added tothe mixture and placed on the array under a glass coverslip. Slides wereincubated for 18 hours at 42° C. in a humid hybridization cabinet (cat#:RPK0176; Amersham BioSciences, UK). Post-hybridization washing wasperformed for 10 minutes at 56° C. in 1×SSC, 0.1% SDS, two times for 10minutes at 56° C. in 0.1×SSC, 0.1% SDS and for 2 minutes at 37° C. in0.1×SSC.

Scanning and Data Analysis

Arrays were scanned at 532 nm and 635 nm using a Generation III scanner(Amersham BioSciences, UK). Image analysis was performed withArrayVision (Imaging Research Inc, Ontario, Canada). Spot intensitieswere measured as artifact removed total intensities (ARVol). Nobackground correction was performed. First, within-slide normalizationwas addressed by plotting for each single slide a “MA-plot” (Yang etal., 2002), where M=log₂ (R/G) and A=log₂ 0.54√R×G. The “LOWESS”normalization was applied to correct for dye-intensity differences.Subsequently, in order to normalize between slides and to identifydifferentially expressed genes between the two genotypes, two sequentialanalyses of variance (ANOVAs) were applied, proposed by Wolfinger et al.(2002), as follows: 1) firstly, the base-2 logarithm of the“LOWESS”-transformed measurements for all 73,264 spots (y_(gklm)) wassubjected to a normalization model of the formy_(iklm)=μ+A_(k)+A_(k)D_(l)R_(m)+ε_(iklm), where μ is the sample mean,A_(k) is the effect of the kth array (k=1-4), A_(k)D_(l)R_(m) is thechannel-effect (AD) for the mth replication of the total collection ofcDNA fragments (m=2; left or right), and ε_(iklm) is the stochasticerror; 2) secondly, the residuals from this model were subjected to4,579 gene-specific models of the formr_(ijkl)=μ+G_(i)A_(k)+G_(i)D_(l)+G_(i)C_(j)+γ_(ijkl) where G_(i)A_(k) isthe spot effect, G_(i)D_(l) is the gene-specific dye effect, G_(i)C_(j)is representing the signal intensity for genes that can specifically beattributed to the genotypes (effect of interest), and γ_(ijkl) is thestochastic error. All effects were assumed to be fixed effects, exceptε_(klm) and γ_(ijkl). A t-test for differences between the G_(i)C_(j)effects was performed, where the t-tests are all based on n₁+n₂−2degrees of freedom corresponding to the n₁ WT hybridizations and n₂E2Fa-DPa hybridisations. The p-value cutoff was set at 0.01. No furtheradjustment for multiple testing was performed, as Bonferroni adjustmentfor 4,579 tests, to assure an experiment-wise false positive rate of0.05, results in a p-value cutoff of 1e^(−5.0), which is certainly tooconservative; therefore it was chosen to set the p-value cutoffarbitrarily at the 0.01 level. Also G_(i)D_(l) effects were estimatedand t-tested for significance at the 1% level in a same way as describedabove. Genes with a significant G_(i)D_(l) effect were discarded.Genstat was used to perform both the normalization and gene model fits.

Example 3 Results of the Microarray Analysis and Statistical Analysis

A micro-array containing in duplicate 4579 unique Arabidopsis ESTs,representing about a sixth of the total genome, was used to compare thetranscriptome of wild type with that of E2Fa-DPa overexpressing plants.cDNA was synthesized from total RNA isolated from wild type andtransgenic plants harvested 8 days after sowing. At this stage,transgenic plants were distinguished from control plants by theappearance of curled cotelydons which display ectopic cell divisions andenhanced endoreduplication (De Veylder et al., 2002). In the first twohybridizations Cy3 and Cy5 fluorescently labeled probe pairs of controland E2Fa-DPa cDNA were used using independent mRNA extractions of theE2Fa-DPa plants. Subsequently, a dye-swap replication was performed forboth hybridizations, resulting in a total of four cDNA microarrayhybridizations.

Fluorescence levels were analyzed with the aim to establish whether thelevel of expression of each gene varied according to overexpression ofthe E2Fa-DPa transcription factor. Two sequential analyses of variance(ANOVAs) were used, as proposed by Wolfinger et al. (2002). The firstANOVA model, called the “normalization” model, accounts forexperiment-wise systematic effects, such as array- and channel-effects,that could bias inferences made on the data from the individual genes.The residuals from this model represent normalized values and are theinput data for the second ANOVA model, called the “gene” model. The genemodels are fit separately to the normalized data from each gene. Thisprocedure uses differences in normalized expression levels, rather thanratios, as the unit of analysis of expression differences.

Prior to the estimation of genotype-specific signal intensities of thegenes (G_(i)C_(j) effects), which are the effects of interest,gene-specific dye effects (G_(i)D_(l) effects) were estimated andt-tested for significance at the 1% level. One hundred and thirty onegenes showed a significant G_(i)D_(l) effect and were discard fromfurther analysis. For each of the remaining 4,448 genes on the arrays, at-test on the G₁C_(j) effects for significant differences (p<0.05) wasperformed. FIG. 1 plots the obtained p-values (as the negative log10 ofthe p-value) against the magnitude of the effect (log2 of estimated foldchange). This volcano plot illustrates the substantial differencesignificance testing can make versus cutoffs made strictly on the basisof the fold change. The two vertical reference lines indicate a 2-foldcutoff for either repression or induction, while the horizontalreference line refers to the p-value cutoff at the 0.05 value. Thesereference lines divide the plot into six sectors. The 3,535 genes in thelower middle sector have low significance and low fold change, and bothmethods agree that the corresponding changes are not significant. The188 genes in the upper left and right sectors have high significance(p<0.05) and high fold change (≧2); 84 of these genes show a significanttwo-or-more-fold induction of expression, where the remaining 104 genesshow a significant two-or-more-fold repression of expression in theE2Fa-DPa plant. Finally, the 715 genes in the upper middle sectorrepresent significant (p<0.05) up- or downregulated genes, but with alow (≦2) fold change. The full dataset of genes can be viewed athttp://www.psb.rug.ac.be/E2F, which dataset is incorporated herein byreference.

All the sequences that are 1.3 times upregulated (ratio of more than1.999) in E2Fa-DPa overexpressing plants are presented in Table 4. Allthe sequences that are 1.3 times repressed (calculated as 1/ratio ofless than 0.775) are presented in Table 5. Particularly interestinggenes that are more than 2-fold upregulated or 2 fold repressed areselected and separately represented in Tables 1 and 2.

Example 4 Sequencing and RT Mediated PCR Analysis

The identity of the genes was confirmed by sequencing, and the inductionof a random set of genes was confirmed by RT-PCR analysis (FIG. 5).

RNA was isolated from plants 8 days after sowing with the Trizol reagent(Amersham Biosciences). First-strand cDNA was prepared from 3 μg oftotal RNA with the Superscript RT II kit (Invitrogen) and oligo(dT)18according to the manufacturer's instructions. A 0.25 μl aliquot of thetotal RT reaction volume (20 μl) was used as a template in asemi-quantitative RT-mediated PCR amplification, ensuring that theamount of amplified product remained in linear proportion to the initialtemplate present in the reaction. From the PCR reaction, 10 μl wasseparated on a 0.8% agarose gel and transferred onto Hybond N+ membranes(Amersham Biosciences) that were hybridized at 65° C. withfluorescein-labeled probes (Gene Images random prime module; AmershamBiosciences). The hybridized bands were detected with the CDP Stardetection module (Amersham Biosciences). Primers used were5′-AAAAAGCAGGCTGTGTCGTACGATCTTCTCCCGG-3′ (SEQ ID NO 2757) and 5′-AGAAAGCTGGGTCATGTGATAGGAGAACCAGCG-3′ (SEQ ID NO 2758) for E2Fa, 5′-ATAGAATTCGCTTACATTTTGAAACTGATG-3′ (SEQ ID NO 2759) and 5′-ATAGTCGACTCAGCGAGTATCAATGGATCC-3′ (SEQ ID NO 2760) for DPa, 5′-CAGATCTTGTTAACCTTGACATCTCAG-3′ (SEQ ID NO 2761) and 5′-GGGTCAAAAGATACAACCACACCAG-3′ (SEQ ID NO2762) for glutamine synthetase (GS), 5′-GGTTTACGAGCTACATGGCCC-3′ (SEQ IDNO 2763) and 5′-GAGCAATCCGTTCAGCCTCC-3′ (SEQ ID NO 2764) for glutamatesynthase (GOGAT), 5′-GCGTTTGACCACTCTTGGAGAC-3′ (SEQ ID NO 2765) and5′-GAACGCCA TTGAGAAAGTCCGC-3′ (SEQ ID NO 2766) for histone acetylase HATB, 5′-GTTACCGG CTCGACTTGAAGATC-3′ (SEQ ID NO 2767) and5′-GAATCGGAGGGAAAGTCTGACG-3′ (SEQ ID NO 2768) for LOB domain protein 41,5′-GTGTGGTTTCCAAGCTTTCCTACG-3′ (SEQ ID NO 2769) and5′-GGTGAAGGGACTAGCCTTGTGG-3′ (SEQ ID NO 2770) for isocitrate lyase,5′-GGGATCAATCCTCAGGAGAAGG-3′ (SEQ ID NO 2771) and5′-CCGTCCATCTTTATTAGCGGCATG-3′ (SEQ ID NO 2772) for nitrite reductase(NiR), and 5′-TTACCGAGGCTCCTCTTAACCC-3′ (SEQ ID NO 2773) and5′-ACCACCGATCCAGACA CTGTAC-3′ (SEQ ID NO 2774) for actin 2 (ACT2).

Example 5 Characterization of the Genes Identified as Being Involved inE2F/DP Regulated Cellular Processes

The genes of the present invention identified from the microarrayexperiment of Example 2 have unique identification numbers (MIPSaccession number e.g. At1g57680). The MIPS accession number is widelyaccepted in this field as it directly refers to the genomic sequence andthe location of the sequence in the Arabidopsis thaliana genome.Accession numbers are allocated by the Munich Information Center forProtein Sequences (MIPS) and are stored in the MIPS Arabidopsisdatabase. Publicly available sequence and annotation data from all otherAGI (“Arabidopsis Genome Initiative”) groups are included to establish aplant genome database (Schoof H. et al. (2002)). The MIPS Arabidopsisdatabase can be accessed via the Internethttp://mips.gsf.de/cgi-bin/proj/thal and the database can be searchedwith the protein entry code (e.g. At1g57680). An example of the type ofsequence information and protein domain information that is provided fora certain sequence in the MIPS database is shown FIG. 4.

An additional blast search with the genes according to the presentinvention was performed on public databases containing sequences fromother plant species and other organisms. For some of the genesidentified by the microarray, significant levels of homology (lowE-values) were found with sequences from other organisms (see Tables 1and 2 with reference to their Genbank accession number). So far, mainlycorn and rice homologues were identified, but as more genomes will besequenced in the future, many more homologues will be identifiable bythe person skilled in the art as useful in the methods of the presentinvention.

DNA Replication and Cell Cycle Genes

Genes up or downregulated in the E2Fa-DPa overexpressing plants can beclassified into clear groups according their function (Tables 1 and 2).14 Genes that are 2-fold or more upregulated belong to the class ofgenes involved in DNA replication and modification, correlating with theobservation that E2Fa-DPa overexpression plants undergo extensiveendoreduplication. Most of these genes have previously be shown to beupregulated by E2F-DP overexpression in mammalian systems including aputative thymidine kinase, replication factor c, and histone genes (4different ones). Other E2Fa-DPa induced S phase genes include a linkerhistone protein, the topoisomerase 6 subunit A and two subunits of thehistone acetyltransferase HAT B complex, being HAT B and Msi3. The HAT Bcomplex is responsible for the specific diacethylation of newlysynthesized histone H4 during nuclease assembly on newly synthesized DNA(Lusser et al., 1999). Also a DNA methyltransferase responsible for themethylation of cytosine in cells that progress though S phase wasidentified among upregulated genes.

Besides the overexpressed E2Fa gene (being 90-fold more abundant in theE2FaPa overexpressing plants, compared to control plants), only one cellcycle gene (CDKB1;1) shows a 2-fold or more change in expression levelupon E2Fa-DPa overexpression. CDKB1;1 was previously predicted to be acandidate E2F-DP target by virtue of a consensus E2F-DP-binding site inits promoter (de Jager et al., 2001). Whereas CDKB1;1 activity ismaximum at the G2/M transition, its transcript levels start to riseduring late S-phase (Porceddu et al., 2001; Menges and Murray, 2002).Upregulation of CDKB1;1 might therefore be a mechanism to link DNAreplication with mitosis.

Cell Wall Biogenesis Genes

Four members of the xyloglucan endotransglucosylase (XET) gene familywere found to be 2-fold or more upregulated in E2Fa-DPa overexpressingplants, one of them identical to the Meri-5 gene (Medford et al., 1991).XETs are enzymes that modify cell wall components and therefore play alikely role in altering size, shape and physical properties of plantcells. Reversal breakage of the xyloglucan tethers by XETs has beenproposed to be a mechanism for allowing cell wall loosening inturgor-driven cell expansion (Campbell and Braam, 1999). However, thereare several reasons to believe that E2Fa-DPa induced XETs are notrequired for cell expansion. First, cells divide more frequently inE2Fa-DPa overexpressing plants, but the overall cell size of the cellsis smaller. Therefore, no overall increase in expansion-rates is needed.Second, correlated with the absence of increased cell expansion in thetransgenic lines, no induction of genes with a known role in thisprocess, such as expansins, can be seen. Therefore, the hydrolyticactivity of the XETs might be required to incorporate the newlysynthesized cell walls formed during cytokinesis into the existing cellwall structure. Alternatively, as XET activity has shown to be involvedin the postgerminative mobilization of xyloglucan storage reverses inNasturtium cotelydons (Farkas et al., 1992; Fanutti et al., 1993),induction of XETs in E2Fa-DPa overexpressing plants might relate topolysaccharide breakdown to serve the metabolic and energy needs whichare required to synthesize new nucleotides (see below).

Interestingly, two XETs were identified in the set of 2-fold or moredownregulated genes. These XETs are more related to each other than tothe induced XET proteins. This differential response of XETs towards theE2Fa/DPa induced phenotypes suggests that plant XETs can be classifiedin at least 2 different functional classes.

Genes Involved in Metabolism and Biogenesis

Both the group of up and down regulated genes contains a relative largegroup of genes involved in metabolism and biogenesis. Most remarkable isthe induction of genes involved in nitrogen assimilation, such asnitrate reductase (NIA2) (see FIG. 2), glutamine synthetase (GS), andglutamate synthetase (GOGAT). Although not present on the microarray,the nitrite reductase (NiR) gene was found to be induced in thetransgenic line, as demonstrated by RT-mediated PCR analysis. Nitrogenand nitrite reductase catalyse the first step in the nitrogenassimilation pathway, whereas glutamine and glutamate synthetase areinvolved in both the primary assimilation from nitrogen asreassimilation of free ammonium, supplying all plants nitrogen neededfor the biosynthesis of amino-acids and other nitrogen-containingcompounds.

There are other indications that nitrogen metabolism is altered inE2Fa-DPa overexpressing plants, such as the modification of genesreported to be involved in Medicago induced nodulation (MTN3 and anodulin-like gene); and the downregulation of genes involved in sulfurassimilation (adenylylsulfate reductase (APR; 2 different genes) and aputative adenine phosphosulfate kinase). Genes involved in sulfurassimilation such as APR have previously been shown to betranscriptionally downregulated during nitrogen deficiency (Koprivova etal., 2000).

Upregulation of nitrogen assimilation genes in E2Fa-DPa overexpressingplants might reflect the need for nitrogen for nucleotide biosynthesis,as purine and pyrimidine bases are nitrogen-rich. If nitrogenassimilation was indeed stimulated by E2Fa/DPa overexpression, tworequirements should be fulfilled. Since nitrogen assimilation throughthe GS/GOGAT pathway requires α-ketogluterate (Lancien et al., 2000), afirst requirement is that there should be enough α-ketogluterate to actas acceptor molecule for ammonium. Secondly, because assimilation ofnitrogen is energy consuming, the rate of reductant production should behigher in an E2Fa/DPa transgenic than in wild-type plants.

Our micro-array data suggest that in the E2Fa-DPa overexpressing plants,α-ketogluterate accumulation is stimulated in different ways. First,α-ketogluterate production is improved by increased photosyntheticactivity, as indicated by the 4.7-fold upregulation of large subunit ofribulose-1,5-bisphosphate carboxylase/oxygenase (FIG. 2). This resultsin an accumulation of glyceraldehyde-3-phosphate.Glyceraldehyde-3-phosphate can be converted intofructuse-1,6-bisphosphate by fructose bisphosphate aldolase. However, a6-fold downregulation of the fructose bisphosphate aldolase gene rathersuggests the conversion of glyceraldehyde-3-phosphate into pyruvate,which can be converted into α-ketogluterate during glycolysis in thecitrate cycle. The preferential conversion of glyceraldehyde-3-phosphateinto pyruvate in favour of sugars fits the higher need for amino-acidsthan for sugars for nucleotide biosynthesis. A shortage forribose-5-phosphate for nucleotide synthesis is also evident from adownregulation of sucrose-phosphate synthase, resulting in decreasedconversion of fructose-6-phosphate and glucose-6-phosphate into sucrose(FIG. 2).

A second source of α-ketogluterate is provided in the glyoxylate cycleby the 3.1 fold increase in expression of isocitrate lyase, suggestingan increased lipid turnover in E2Fa-DPa overexpressing plants.Isocistrate lyase activity cleaves isocitrate into glyoxylate andsuccinate (FIG. 2). Whereas the formed glyoxylate can be converted intoglycine, which is also required for nucleotide biosynthesis, succinatecan be converted into α-ketogluterate in the citrate cycle. A 2.3-folddecrease of the fumarase gene presumably stimulates the conversion ofproduced α-ketogluterate into glutamate by causing an accumulation ofsuccinate and fumarate, which is also a side product formed duringnucleotide biosynthesis (FIG. 2).

Assimilation of nitrogen is energy consuming. When rates of nitratereduction are high, this pathway becomes the major sink for reductant.About 10% of the electron flux in photosynthesizing leaves is used fornitrate reduction. The amount of required reductant, which in leavesoriginates from electronic photosynthetic electron transport, istherefore expected to be higher in the E2Fa-DPa transgenics.Correspondingly, several components of the chloroplast electrontransport chain and associated ATP-synthesing apparatus, such ascytochrome B6, a PSII subunit and the ATPase epsilon subunit areupregulated in the transgenic plants. Increased expression of theprotochlorophyllide reductase precursor suggests that an increase inchlorophyll biosynthesis is stimulated in E2Fa-DPa overexpressingplants.

Famine of nitrogen has a putative impact on amino-acid biosynthesis, asthree different amino-acid aminotransferases, are downregulated inE2Fa-DPa overexpressing plants. Accompanied with a putative decreasedaminotransferase activity is the observed reduction in expression of anenzyme involved in pyridoxine biosynthesis. Shortage of nitrogen-richamino-acids is also evident from reduced expression of genes encodingvegetative storage proteins (VSP1 and VSP2); and ERD10, a protein with acompositional bias towards glu (Kiyosue et al., 1994). Additionalevidence for amino acid shortage comes from downregulation of amyrosinase-binding protein and cytochrome P450 monooxygenase CYP83A1.Both proteins are involved in the biosynthesis of glucosinolates, beingnitrogen and sulfur containing products derived from amino-acids(Wittstock and Halkier, 2002).

Transcription Factors and Signal Transduction

A total of 4 transcription factors were identified among the genes being2-fold or more upregulated, including two homeobox domain transcriptionfactors. Among them the anthocyaninless2 (ANL2) gene was identified,which is involved in anthocyanin accumulation in subepidermal leaf cells(Kubo et al., 1999). The lack of an obvious increase in anthocyaninaccumulation in E2Fa-DPa overexpressing plants suggests a role for theANL2 protein in plant development different from anthocyanin production.This hypothesis is substantiated by the observation that anl2 mutantplants contain extra cells in the root between the cortical andepidermal layers (Kubo et al., 1999).

The second upregulated homeobox domain transcription factor is Atbh-6.Expression of Atbh-6 is restricted to regions of cell division and/ordifferentiation and has been shown to be inducible by water stress andABA (Soderman et al., 1999). Other putative ABA sensitive genes can berecognized among the E2Fa-DPa induced clones, as well as the coldregulated protein COR6.6, a seed imbitition-like protein and adormancy-associated protein. Here again, changes in expression level ofthese genes might be correlated with modifications in carbon metabolism.A link between ABA and sugar signaling is evident from theidentification of several loci involved in both sugar and hormonalresponses (Finkelstein and Gibson, 2002). Alternatively, it might be theoccurrence of enhanced endoreduplication and/or cell division itselfthat causes a change in the osmotic potential.

Among the downregulated transcription factors a DOF family member ispresent. Many DOF transcription factors are participating in theregulation of storage protein genes and genes involved in carbonmetabolism (Gualberti et al., 2002). Its downregulation might thereforebe linked with the shortage of amino-acids due to the high demand ofnitrogen for nucleotide biosynthesis.

Other regulatory genes modified in E2Fa-DPa overexpressing plantsinclude protein kinases, several putative receptor kinases, a putativephytochrome A, and WD40 repeat containing proteins (Tables 1 and 2).Interestingly, a SNF1-like kinase is downregulated 2-fold in E2Fa-DPaoverexpressing plants. In addition to its proposed role in sugarsignaling, the SNF1 kinase also negatively regulates the activity ofplant nitrate reductase (Smeekens, 2000).

Example 6 Endoreduplication Levels of E2Fa-DPa Plants are NitrogenDependent

The modified expression of a large number of metabolic and regulatorygenes, directly or indirectly linked to nitrogen metabolism, suggests adirect relationship between the high endoreduplication levels found inthe E2Fa/DPa transgenic plants and nitrogen availability. To test thishypothesis, wild type and transgenic plants were grown on mediumcontaining different levels of ammoniumnitrate, ranging from 0.1 to 50mM. Eight days after germination ploidy levels in these plants wasdetermined by flow cytometry. Increasing ammoniumnitrate levels hardlyhad an effect on the ploidy distribution pattern in wild type plants(FIG. 3A). In contrast, in the E2Fa-DPa transgenic plants increasingammoniumnitrate levels resulted in a reproducible and significantincrease in the amount of 32C and 64C nuclei (FIG. 3B). Comparing thelowest with the highest concentration of ammonimumnitrate, an increaseof 32C from 2.0 (±0.3) % to 6.5 (±1.5) %, and of 64C from 0.7 (±0.3) %to 2 (±0.5) % can be seen. Increasing ammonium levels did not have anyeffect on the plant phenotype, as plants remained small with curledleaves on all concentrations of nitrogen tested. These data indicatethat the endoreduplication levels in the E2Fa-DPa overexpressing plantsare limited by nitrogen availability, and that an excess of nitrogen isincorporated into new DNA than in other nitrogen containing compounds.

Example 7 Promoter Analysis of E2Fa-DPa Regulated Genes

Promoter Analysis

The intergenic sequence corresponding to the promoter area of each genespotted on the microarray was extracted from genomic sequences. Thesegenomic sequences are easily accessible for example from the MIPS MatDBdatabase (http://mips.gsf.de/proj/thal/db/). From those intergenicsequences, up to 500 bp upstream of the ATG start codon were extractedand subjected to motif searches in order to retrieve potential E2Felements. Both position and frequency of occurrence was determined usingthe publicly available execuTable of MatInspector (version 2.2) usingmatrices extracted from PlantCARE and matrices made especially for thisparticular analysis (Lescot et al., 2002). The relevance of each motifwas evaluated against a background consisting of all the sequences fromthe dataset.

Results

To distinguish in the present data set the putative direct target genesof E2Fa-DPa from the secondary induced genes, the first 500 bp upstreamof the ATG start codon of the genes with 2-fold or more change inexpression was scanned for the presence of a E2F-like binding sitematching the sequence (A/T)TT(G/C)(G/C)C(G/C)(G/C) (SEQ ID NO 2775). Ofall the different permutations possible, only the TTTCCCGC (SEQ ID NO2776) element was statistically enriched in the set of E2Fa-DPaupregulated genes, suggesting it is the preferred binding site of theE2Fa-DPa complex (Table 3). Moreover, target genes containing thiselement belong mainly to the group of genes involved in DNA replicationand modification, being the main group of target genes in mammaliansystems. These data illustrate that the TTTCCCGC sequence is the mostlikely cis element recognized by E2Fa-DPa. The observation that not allgenes having this DNA sequence in their promoter suggests that thepresence of the TTTCCCCGC motif is not sufficient to make a generesponsive towards E2Fa-DPa, and that E2Fa-DPa co-operates with otherfactors to activate transcription.

It is not excluded that genes without an E2F-like-binding site are notdirectly activated by E2Fa-DPa. Chromatin immunoprecipitationexperiments have shown that mammalian E2F factors can bind to promoterswithout a clear E2F recognition motif (Kiyosue et al., 1994), suggestingthat E2FDP might recognize non-canonical binding sites, or might berecruited by promoters through the association of other factors. In thisrespect, the Chlorella vulgaris nitrate reductase gene, of which theArabidopsis homologue was shown herein to be induced by E2F-DPa, bindsan E2F-DP complex, although a clear consensus binding site is lacking(Cannons and Shiflett, 2001).

E2F can Activate as Well as Repress Promoter Activity.

In the Nicotiana benthamiana PCNA promoter a E2F sequence was identifiedacting as a negative regulatory element during development (Egelkrout etal., 2001). Also the tobacco ribonucleotide reductase small subunit genecontains a E2F element working as a repressor outside the S-phase(Chaboute et al., 2000). In the set of downregulated genes no particularenrichment of a specific E2F sequence could be seen (Table 3). Thereforethe inventors believe that the E2Fa-DPa complex mainly works as atranscriptional activator, and that other E2F-DP complexes are involvedin E2F-mediated transcriptional repression.

Example 8 Individual Characterization of Some Genes Identified by theMethod of the Present Invention

The genes characterized hereunder, are particularly useful for makingplants with improved growth characteristics. These preferred genes areintroduced into a plant and upregulated or downregulated in order tosimulate E2Fa/DPa effects and/or to alter one or more characteristics ofa plant. The particular growth characteristic that may be influenced bythese genes, is described in the following paragraphs by reference tothe biological function of that particular gene.

At1g07000 Showing Homology to Leucine Zipper

At1g07000 is a potential leucine zipper that is not preceded by a basicdomain. The leucine zipper consists of repeated leucine residues atevery seventh position and mediates protein dimerization as aprerequisite for DNA-binding. The leucines are directed towards one sideof an alpha-helix. The leucine side chains of two polypeptides arethought to interdigitate upon dimerization (knobs-into-holes model). Theleucine zipper may dictate dimerization specificity.

Leucine zippers are DNA binding protein with dimerization properties,having important functions in development and stress tolerance inplants.

At1g09070 Showing Homology to Soybean Cold Regulate Gene SRC2

This genes and its expressed protein is predicted in Arabidopsis, rice,corn, soybean, however, based on a homology search using the BLASTprogram, no functional homologue was known, not even a clear animalhomologue, so no clear function can be predicted for this gene orprotein (Takahashi, R. and Shimosaka, E. (1997)).

At1 g21690 Showing Homology to Replication Factor

Replication factor C(RFC) is a pentameric complex of five distinctsubunits that functions as a clamp loader, facilitating the loading ofproliferating cell nuclear antigen (PCNA) onto DNA during replicationand repair. More recently the large subunit of RFC, RFC (p140), has beenfound to interact with the retinoblastoma (Rb) tumor suppressor and theCCAAT/enhancer-binding protein alpha (C/EBPalpha) transcription factor.It is reported that RFC (p140) associates with histone deacetylaseactivity and interacts with histone deacetylase 1 (HDAC1) (Anderson, L.A. and Perkins, N. D. (2002); Furukawa, T. et al. (2001)) RFC is poorlyknown in plants. It can be important for development for modulating geneexpression during cell cycle at S phase, or through chromatinregulation.

At1g23030 Showing Homology to Armadillo Protein

Members of the armadillo (arm) repeat family of proteins are implicatedin tumorigenesis, embryonic development, and maintenance of tissueintegrity. ARM proteins participate in linking cytoskeleton to membraneproteins and structures. These proteins share a central domain that iscomposed of a series of imperfect 45 amino acid repeats. Armadillofamily members reveal diverse cellular locations reflecting theirdiverse functions. A single protein exerts several functions throughinteractions of its armadillo repeat domain with diverse bindingpartners. The proteins combine structural roles as cell-contact andcytoskeleton-associated proteins and signaling functions by generatingand transducing signals affecting gene expression. The study ofarmadillo family members has made it increasingly clear that adistinction between structural proteins on the one hand and signalingmolecules on the other is rather artificial. Instead armadillo familymembers exert both functions by interacting with a number of distinctcellular-binding partners. Proteins of the armadillo family are involvedin diverse cellular processes in higher eukaryotes. Some of them, likearmadillo, beta-catenin and plakoglobins have dual functions inintercellular junctions and signalling cascades. Others belonging to theimportin-alpha-subfamily are involved in NLS (Nuclear localizationsignal) recognition and nuclear transport, while some members of thearmadillo family have as yet unknown functions. (Wang, Y. X. et al.(2001); Hatzfeld, M. (1999). ARM proteins are key protein binding unitsthat are involved at several steps during development. Some are specificto the cell cycle APC degradation complex. These type of genes have beenpoorly studied in plants, some have been involved in light andgibberellin signaling in potato.

At1g27500 Showing Homology to Kinesin Light Chain.

The motor protein kinesin is a heterotetramer composed of two heavychains of approximately 120 kDa and two light chains of approximately 65kDa protein. Kinesin motor activity is dependent on the presence of ATPand microtubules. Conventional kinesin is prevented from binding tomicrotubules (MTs) when not transporting cargo. The function of LCkinesin is to keep kinesin in an inactive ground state by inducing aninteraction between the tail and motor domains of HC; activation forcargo transport may be triggered by a small conformational change thatreleases the inhibition of the motor domain for MT binding. This proteinis important to regulate movement controlled by microtubules within thecytoplasm, for example the flux of vesicles between the different cellmembrane compartments.

At1g72180 Showing Homology to Putative Receptor Protein Kinase

Plant receptor-like kinases (RLKs) are transmembrane proteins withputative amino-terminal extracellular domains and carboxyl-terminalintracellular kinase domains, with striking resemblance in domainorganization to the animal receptor tyrosine kinases such as epidermalgrowth factor receptor. The recently sequenced Arabidopsis genomecontains more than 600 RLK homologs. Although only a handful of thesegenes have known functions and fewer still have identified ligands ordownstream targets, the studies of several RLKs such as CLAVATA1,Brassinosteroid Insensitive 1, Flagellin Insensitive 2, and S-locusreceptor kinase provide much-needed information on the functionsmediated by members of this large gene family. RLKs control a wide rangeof processes, including development, disease resistance, hormoneperception, and self-incompatibility. Combined with the expressionstudies and biochemical analysis of other RLKs, more details of RLKfunction and signaling are emerging.

At1g72900 Showing Homology to Disease Resistance Protein (TIR VirusResistance Protein)

The TIR gene has been described by Kroczynska, B. et al. (1999).

At2g30590 Showing Homology to WRKY Transcription Factor(Toll/Interleukin-1 Receptor-Like Protein)

The sequence shows homology to tomato Cf-9 resistance gene Avr9/Cf-9rapidly elicited protein 4 (NL27) (Hehl, R. et al. (1998)). WRKYproteins are a large group of transcription factors restricted to theplant kingdom. WRKY proteins are a recently identified class ofDNA-binding proteins that recognize the TTGAC(C/T) W-box elements foundin the promoters of a large number of plant defense-related genes (Dongand Chen, 2003). It has been found that the majority are responsive bothto pathogen infection and to salicylic acid. The functions of all otherWRKY genes revealed to date involve responses to pathogen attack,mechanical stress, and senescence (Dong and Chen, 2003).

At1g80530 Showing Homology to Nodulin

Infection of soybean roots by nitrogen-fixing Bradyrhizobium japonicumleads to expression of plant nodule-specific genes known as nodulins.Nodulin 26, a member of the major intrinsic protein/aquaporin (AQP)channel family, is a major component of the soybean symbiosome membrane(SM) that encloses the rhizobium bacteroid. These results indicate thatnodulin 26 is a multifunctional AQP that confers water and glyceroltransport to the SM, and likely plays a role in osmoregulation duringlegume/rhizobia symbioses (Dean et al. (1999). Rice (Oryza sativa var.Nipponbare) possesses two different homologues of the soybean earlynodulin gene GmENOD93 (GmN93), OsENOD93a (homology of 58.2% toGmENOD93), OsENOD93b (homology of 42.3%). In intact rice tissues,OsENOD93b was most abundantly expressed in roots and at much lowerlevels in etiolated and green leaves, whereas the expression ofOsENOD93a was very low in roots and etiolated leaves, and was notdetected in green leaves. The level of OsENOD93a expression was enhancedmarkedly in suspension-cultured cells, whereas that of OsENOD93b did notincrease (Reddy et al. (1998)). Homologues of genes that are produced inresponse to infection of soybean roots by bacteria are also present inother plants such rice. Their function is largely unknown, somefunctional homologues are identified such as a water channel involved inosmoregulation.

At2g34770 Showing Homology to Fatty Acid Hydroxylase

This gene has been described in Matsuda et al. (2001). A common featureof the membrane lipids of higher plants is a large content ofpolyunsaturated fatty acids, which typically consist of dienoic andtrienoic fatty acids. Two types of omega-3 fatty acid desaturase, whichare present in the plastids and in the endoplasmic reticulum (ER),respectively, are responsible for the conversion of dienoic to trienoicfatty acids. To establish a system for investigating thetissue-specific, and hormone-regulated expression of the ER-typedesaturase gene (FAD3), transgenic plants of Arabidopsis thaliana (L.)Heynh. containing the firefly luciferase gene (LUC) fused to the FAD3promoter (FAD3::LUC) were constructed. The results as discussed in thisreport suggest that the expression of ER-type desaturase is regulatedthrough synergistic and antagonistic hormonal interactions, and thatsuch hormonal regulation and the tissue specificity of the expression ofthis gene are further modified in accordance with the growth phase inplant development (Wellesen K, et al. (2001); Kachroo P, et al. (2001);Kahn, R. A. et al. (2001); Smith, M. et al. (2000)).

At2g43402 Showing Homology to Cinnamoyl CoA Reductase

CCR enzyme is involved in lignification. The CCR transcript is expressedin lignified organs, i.e. root and stem tissues, and is localized mainlyin young differentiating xylem. Also, monolignols may be precursors ofend products other than lignins. CCR catalyses the conversion ofcinnamoyl-CoAs into their corresponding cinnamaldehydes, i.e. the firststep of the phenylpropanoid pathway specifically dedicated to themonolignol biosynthetic branch. The two genes are differentiallyexpressed during development and in response to infection. AtCCR1 ispreferentially expressed in tissues undergoing lignification. Incontrast, AtCCR2, which is poorly expressed during development, isstrongly and transiently induced during the incompatible interactionwith Xanthomonas campestris pv. Campestris leading to a hypersensitiveresponse. Altogether, these data suggest that AtCCR1 is involved inconstitutive lignification whereas AtCCR2 is involved in thebiosynthesis of phenolics whose accumulation may lead to resistance(Lauvergeat et al. (2001)). This protein is involved during development,increase in growth diameter, lignification of vascular strands andinterfascicular fibers.

At2g47440 Showing Homology to Tetratricopeptide Repeat Protein

The tetratricopeptide repeat (TPR) is found in many proteins performinga wide variety of functions, the TPR domain itself is believed to be ageneral protein recognition module. Different proteins may contain from3 to 16 tandem TPR motifs (34 amino acid sequence). It has been shownthat some proteins contain a TPR repeat are cell cycle regulated.

At3g23750 Showing Homology to Receptor Like Kinase TMK

The kinase domain of NtTMK1 contained all of 12 subdomains and invariantamino acid residues found in eukaryotic protein kinases. Theextracellular domain contained 11 leucine-rich repeats, which have beenimplicated in protein-protein interactions. The amino acid sequence ofNtTMK1 exhibited high homology with those of TMK1 of Arabidopsis and TMKof rice in both kinase and extracellular domains, suggesting that NtTMK1is a TMK homologue of tobacco. The NtTMK1 transcripts were present inall major plant organs, but its level varied in different developmentalstages in anthers and floral organs. NtTMK1 mRNA accumulation in leaveswas stimulated by CaCl2, methyl jasmonate, wounding, fungal elicitors,chitins, and chitosan. The NtTMK1 mRNA level also increased uponinfection with tobacco mosaic virus (Cho and Pai (2000)). This proteinis involved in different aspects of development and disease resistance.

At3g61460 Showing Homology to RING H2

RING-finger proteins contain cysteine-rich, zinc-binding domains and areinvolved in the formation of macromolecular scaffolds important fortranscriptional repression and ubiquitination. RING H2 act as E3ubiquitin-protein ligases and play critical roles in targeting thedestruction of proteins of diverse functions in all eukaryotes, rangingfrom yeast to mammals. The Arabidopsis genome contains a large number ofgenes encoding RING finger proteins. A small group is constituted bymore than 40 RING-H2 finger proteins that are of small size, not morethan 200 amino acids, and contain no other recognizable protein-proteininteraction domain(s). This type of genes is very important for severalaspect of development, regulation of developmental proteins, cell cycleproteins.

At4g00730 Showing Homology to Homeodomain AHDP (Antocyaninless 2)

This is a homeodomain transcription factor; similar to ATML1 and is veryconserved and has epidermis specific expression. This sequence showsalso homology to Zea mays mRNA for OCL3 protein (Ingram, G. C. et al.(2000)).

At4g13940 Showing Homology to Adenosylhomocysteinase (GlutathioneDependent Formaldehyde Dehydrogenase)

Glutathione-dependent formaldehyde dehydrogenase was described inSakamoto, A. et al. (2002), Arabidopsis glutathione-dependentformaldehyde dehydrogenase is an S-nitrosoglutathione reductase.S-Nitrosoglutathione (GSNO), an adduct of nitric oxide (NO) withglutathione, is known as a biological NO reservoir. Heterologousexpression in Escherichia coli of a cDNA encoding aglutathione-dependent formaldehyde dehydrogenase of Arabidopsis thalianashowed that the recombinant protein reduces GSNO. The identity of thecDNA was further confirmed by functional complementation of thehypersensitivity to GSNO of a yeast mutant with impaired GSNOmetabolism. This is the first demonstration of a plant GSNO reductase,suggesting that plants possess the enzymatic pathway that modulates thebioactivity and toxicity of NO.

At4g35050 Showing Homology to WD40 MSI3

Members of the MSI/RbAp sub-family of WD-repeat proteins are widespreadin eukaryotic organisms and form part of multiprotein complexes that areinvolved in various biological pathways, including chromatin assembly,regulation of gene transcription, and cell division. The Zea maysRbAp-like protein (ZmRbAp1) binds acetylated histones H3 and H4 andsuppresses mutations that have a negative effect on the Ras/cAMP pathwayin yeast. The ZmRbAp genes form a gene family and are expressed indifferent tissues of Z. mays L. plants. Determination of its expressionpattern during maize seed development revealed that ZmRbAp transcriptsare abundant during the initial stages of endosperm formation. Inaddition, the transcripts are specifically localized in shoot apicalmeristem and leaf primordia of the embryo. ZmRbAp genes play a role inearly endosperm differentiation and plant development (Rossi et al.(2001)). Also Rb proteins are known to be involved in multi-proteincomplexes; there are Rb binding protein characterized; and Rb plays arole in chromatin remodeling and cell cycle control and is important indevelopment and growth of organs. The retinoblastoma (RB) proteinregulates G1 progression and functions through its association withvarious cellular proteins. Two closely related mammalian RB bindingproteins, RbAp48 and RbAp46, share sequence homology with the Msi1protein of yeast. MSI1 is a multicopy suppressor of a mutation in theIRA1 gene involved in the Ras-cAMP pathway that regulates cellulargrowth. Human RbAp48 is present in protein complexes involved in histoneacetylation and chromatin assembly. Four plant RbAp48- and Msi1-likeproteins have been identified: one from tomato, LeMSI1, and three fromArabidopsis. LeMSI1 can function as a multicopy suppressor of the yeastiral mutant phenotype. The LeMSI1 protein localizes to the nucleus andbinds to a 65-kD protein in wild-type as well as ripening inhibitor(rin) and Neverripe (Nr) tomato fruit. LeMSI1 also binds to the human RBprotein and the RB-like RRB1 protein from maize, indicating that thisinteraction is conserved between plants and animals (Ach et al. (1997)).

At4g36670 Showing Homology to Sugar Transporter

The ERD6 clone is expressed after exposure to dehydration stress for 1h. The ERD6 is related to sugar transporters of bacteria, yeasts, plantsand mammals. Hydropathy analysis revealed that ERD6 protein has 12putative transmembrane domains and a central hydrophilic region.Sequences that are conserved at the ends of the 6th and 12thmembrane-spanning domains of sugar transporters are also present inERD6. ERD6 gene is a member of a multigene family in the Arabidopsisgenome. The expression of the ERD6 gene was induced not only bydehydration but also by cold treatment (Kiyosue et al. (1998)).

At5g01870 Showing Homology to Lipid Transfer Protein

Nonspecific lipid transfer proteins (LTPs) from plants are characterizedby their ability to stimulate phospholipid transfer between membranes invitro. However, because these proteins are generally located outside ofthe plasma membrane, it is unlikely that they have a similar role invivo. The LTP1 promoter was active early in development in protodermcells of embryos, vascular tissues, lignified tips of cotyledons, shootmeristem, and stipules. In adult plants, the gene was expressed inepidermal cells of young leaves and the stem. In flowers, expression wasobserved in the epidermis of all developing influorescence and flowerorgan primordial the epidermis of the siliques and the outer ovule wall,the stigma, petal tips, and floral nectaries of mature flowers, and thepetal/sepal abscission zone of mature siliques. Consistent with a rolefor the LTP1 gene product in some aspect of secretion or deposition oflipophilic substances in the cell walls of expanding epidermal cells andcertain secretory tissues. The LTP1 promoter region contained sequenceshomologous to putative regulatory elements of genes in thephenylpropanoid biosynthetic pathway, suggesting that the expression ofthe LTP1 gene may be regulated by the same or similar mechanisms asgenes in the phenylpropanoid pathway (Thoma, S. et al. (1994)). Morebackground knowledge to this type of genes can be found in the followingreferences: Clark, A. M. et al., (1999); Toonen, M. A. et al. (1997);Molina, A. (1997); Thoma, S. et al. (1994).

At5g02820 Showing Homology to SPO Like

Plant steroid hormones, such as brassinosteroids (BRs), play importantroles throughout plant growth and development. Plants defective in BRbiosynthesis or perception display cell elongation defects and severedwarfism. Two dwarf mutants named bin3 and bin5 with identicalphenotypes to each other display some characteristics of BR mutants andare partially insensitive to exogenously applied BRs. In the dark, bin3or bin5 seedlings are de-etiolated with short hypocotyls and opencotyledons. Light-grown mutant plants are dwarfs with short petioles,epinastic leaves, short inflorescence stems, and reduced apicaldominance. BIN3 and BIN5 were cloned and show that BIN5 is one of threeputative Arabidopsis SPO11 homologs (AtSPO11-3) that also sharessignificant homology to archaebacterial topoisomerase VI (TOP6) subunitA, whereas BIN3 represents a putative eukaryotic homolog of TOP6B. Thepleiotropic dwarf phenotypes of bin5 establish that, unlike all of theother SPO11 homologs that are involved in meiosis, BIN5/AtSPO11-3 playsa major role during somatic development. Furthermore, microarrayanalysis of the expression of about 5500 genes in bin3 or bin5 mutantsindicates that about 321 genes are down-regulated in both of themutants, including 18 of 30 BR-induced genes. These results suggest thatBIN3 and BIN5 may constitute an Arabidopsis topoisomerase VI thatmodulates expression of many genes, including those regulated by BRs(Yin Y et al. (2002)). More background information on this type of genecan be found in the following references: Soustelle, C. et al. (2002);Kee, K. and Keeney, S. (2002); Hartung, F. and Puchta, H. (2001);Grelon, M. et al. (2001).

At5g14420 Showing Homology to Copine I (Phospholipid Binding Protein)

The copines are a newly identified class of calcium-dependent,phospholipid binding proteins that are present in a wide range oforganisms, including Paramecium, plants, Caenorhabditis elegans, mouse,and human. However, the biological functions of the copines are unknown.A humidity-sensitive copine mutant was made in Arabidopsis and undernon-permissive, low-humidity conditions, the cpn1-1 mutant displayedaberrant regulation of cell death that included a lesion mimic phenotypeand an accelerated hypersensitive response (HR). However, the HR incpn1-1 showed no increase in sensitivity to low pathogen titers.Low-humidity-grown cpn1-1 mutants also exhibited morphologicalabnormalities, increased resistance to virulent strains of Pseudomonassyringae and Peronospora parasitica, and constitutive expression ofpathogenesis-related (PR) genes. Growth of cpn1-1 under permissive,high-humidity conditions abolished the increased disease resistance,lesion mimic, and morphological mutant phenotypes but only partiallyalleviated the accelerated HR and constitutive PR gene expressionphenotypes. The disease resistance phenotype of cpn1-1 suggests that theCPN1 gene regulates defense responses. Alternatively, the primaryfunction of CPN1 may be the regulation of plant responses to lowhumidity, and the effect of the cpn1-1 mutation on disease resistancemay be indirect (Jambunathan et al. (2001)). Arabidopsis growth over awide range of temperatures requires the BONZAI1 (BON1) gene because bon1null mutants make miniature fertile plants at 22° C. but have wild-typeappearance at 28° C. The expression of BON1 and a BON1-associatedprotein (BAP1) is modulated by temperature. Thus BON1 and BAP1 may havea direct role in regulating cell expansion and cell division at lowertemperatures. BON1 contains a Ca(2+)-dependent phospholipid-bindingdomain and is associated with the plasma membrane. It belongs to thecopine gene family, which is conserved from protozoa to humans. The datahere obtained suggest that this gene family may function in the pathwayof membrane trafficking in response to external conditions (Hua et al.(2001)). The major calcium-dependent, phospholipid-binding proteinobtained from extracts of Paramecium tetraurelia, named copine, had amass of 55 kDa, bound phosphatidylserine but not phosphatidylcholine atmicromolar levels of calcium but not magnesium, and promoted lipidvesicle aggregation. Current sequence databases indicate the presence ofmultiple copine homologs in green plants, nematodes, and humans. Thefull-length sequences reveal that copines consist of two C2 domains atthe N terminus followed by a domain similar to the A domain thatmediates interactions between integrins and extracellular ligands. Theassociation with secretory vesicles, as well the general ability ofcopines to bind phospholipid bilayers in a calcium-dependent manner,suggests that these proteins may function in membrane trafficking(Creutz et al. (1998)).

At5g49160 Showing Homology to Cytosine Methyltransferase

DNMT3L is a regulator of imprint establishment of normally methylatedmaternal genomic sequences. DNMT3L shows high similarity to the de novoDNA methyltransferases, DNMT3A and DNMT3B, however, the amino acidresidues needed for DNA cytosine methyltransferase activity have beenlost from the DNMT3L protein sequence. Apart from methyltransferaseactivity, Dnmt3a and Dnmt3b serve as transcriptional repressorsassociating with histone deacetylase (HDAC) activity. DNMT3L can alsorepress transcription by binding directly to HDAC1 protein. PHD-likezinc finger of the ATRX domain is the main repression motif of DNMT3L,through which DNMT3L recruits the HDAC activity needed fortranscriptional silencing. DNMT3L as a co-repressor protein and suggestthat a transcriptionally repressed chromatin organisation through HDACactivity is needed for establishment of genomic imprints (Aapola et al.(2002)). More background information on this type of gene can be foundin Chen, T. et al. (2002); Bartee, L. and Bender, J. (2001); Freitag M.et al. (2002). In Arabidopsis a SWI2/SNF2 chromatin remodelingfactor-related protein DDM1 and a cytosine methyltransferase MET1 isrequired for maintenance of genomic cytosine methylation. Mutations ineither gene cause global demethylation. There are also effects of thesemutations on the PAI tryptophan biosynthetic gene family, which consistsof four densely methylated genes arranged as a tail-to-tail invertedrepeat plus two unlinked singlet genes. The methylation mutations causedonly partial demethylation of the PAI loci: ddm1 had a strong effect onthe singlet genes but a weaker effect on the inverted repeat, whereasmet1 had a stronger effect on the inverted repeat than on the singletgenes. The double ddm1 met1 mutant also displayed partial demethylationof the PAI genes, with a pattern similar to the ddm1 single mutant. Todetermine the relationship between partial methylation and expressionfor the singlet PAI2 gene a novel reporter strain of Arabidopsis wasconstructed, in which PAI2 silencing could be monitored by a bluefluorescent plant phenotype diagnostic of tryptophan pathway defects.This reporter strain revealed that intermediate levels of methylationcorrelate with intermediate suppression of the fluorescent phenotype.Other background information can be found in Finnegan, E. J. and KovacK. A. (2000). Plant DNA methyltransferases. DNA methylation is animportant modification of DNA that plays a role in genome management andin regulating gene expression during development. Methylation is carriedout by DNA methyltransferases which catalyse the transfer of a methylgroup to bases within the DNA helix. Plants have at least three classesof cytosine methyltransferase which differ in protein structure andfunction. The METI family, homologues of the mouse Dnmtlmethyltransferase, most likely function as maintenancemethyltransferases, but may also play a role in de novo methylation. Thechromomethylases, which are unique to plants, may preferentiallymethylate DNA in heterochromatin; the remaining class, with similarityto Dnmt3 methyltransferases of mammals, are putative de novomethyltransferases. The various classes of methyltransferase may showdifferential activity on cytosines in different sequence contexts.Chromomethylases may preferentially methylate cytosines in CpNpGsequences while the Arabidopsis METI methyltransferase shows apreference for cytosines in CpG sequences. Additional proteins, forexample DDM1, a member of the SNF2/SWI2 family of chromatin remodelingproteins, are also required for methylation of plant DNA.

At5g54940 Showing Homology to Translation Initiation Factor(Translational Initiation Factor eIF1),

Protein synthesis has not been considered to be fundamental in thecontrol of cell proliferation. However, data are emerging on theinvolvement of this process in cell growth and tumorigenesis. Proteinbiosynthesis is a central process in all living cells. It is one of thelast steps in the transmission of genetic information stored in DNA onthe basis of which proteins are produced to maintain the specificbiological function of a given cell. Protein synthesis takes place onribosomal particles where the genetic information transcribed into mRNAis translated into protein. The process of protein synthesis on theribosome consists of three phases: initiation, elongation andtermination. Brassinosteroids (BRs) regulate the expression of numerousgenes associated with plant development, and require the activity of aSer/Thr receptor kinase to realize their effects. In animals, thetransforming growth factor-beta (TGF-beta) family of peptides acts viaSer/Thr receptor kinases to have a major impact on several pathwaysinvolved in animal development and adult homeostasis. TGF-betareceptor-interacting protein (TRIP-1) was previously shown by others tobe an intracellular substrate of the TGF-beta type II receptor kinasewhich plays an important role in TGF-beta signaling. TRIP-1 is aWD-repeat protein that also has a dual role as an essential subunit ofthe eukaryotic translation initiation factor eIF3 in animals, yeast andplants, thereby revealing a putative link between a developmentalsignaling pathway and the control of protein translation. In yeast,expression of a TRIP-1 homolog has also been closely associated withcell proliferation and progression through the cell cycle. Transcriptlevels of TRIP-1 homologs in plants are regulated by BR treatment undera variety of conditions, and transgenic plants expressing antisenseTRIP-1 RNA exhibit a broad range of developmental defects, includingsome that resemble the phenotype of BR-deficient and -insensitivemutants. This correlative evidence suggests that a WD-domain proteinwith reported dual functions in vertebrates and fungi might mediate someof the molecular mechanisms underlying the regulation of plant growthand development by BRs (Jiang and Clouse (2001)). The Arabidopsis COP9signalosome is a multisubunit repressor of photomorphogenesis that isconserved among eukaryotes. This complex may have a general role indevelopment. association between components of the COP9 signalosome(CSN1, CSN7, and CSN8) and two subunits of eukaryotic translationinitiation factor 3 (eIF3), eIF3e (p48, known also as INT-6) and eIF3c(p105). AteIF3e coimmunoprecipitated with CSN7, and eIF3ccoimmunoprecipitated with eIF3e, eIF3b, CSN8, and CSN1. eIF3e directlyinteracted with CSN7 and eIF3c. eIF3e and eIF3c are probably componentsof multiple complexes and that eIF3e and eIF3c associate with subunitsof the COP9 signalosome, even though they are not components of the COP9signalosome core complex. This interaction may allow for translationalcontrol by the COP9 signalosome (Yahalom et al. (2001)).

At5g56740 Showing Homology to Histone Acetyl Transferase HATB

Transforming viral proteins such as E1A which force quiescent cells intoS phase have two essential cellular target proteins, Rb and CBP/p300. Rbregulates the G1/S transition by controlling the transcription factorE2F. CBP/p300 is a transcriptional co-activator with intrinsic histoneacetyl-transferase activity. This activity is regulated in a cell cycledependent manner and shows a peak at the G1/S transition. CBP/p300 isessential for the activity of E2F, a transcription factor that controlsthe G1/S transition. It was found that CBP HAT activity is required bothfor the G1/S transition and for E2F activity. Thus CBP/p300 seems to bea versatile protein involved in opposing cellular processes, whichraises the question of how its multiple activities are regulated(Ait-Si-Ali, S. et al (2000)). The BRCA2 is a histone acetyltransferase.Two potential functions of BRCA2 were proposed which includes role inthe regulation of transcription and also in DNA repair. Forty-five-aminoacid region encoded by exon 3 of BRCA2 was shown to have transcriptionalactivation function. Recent studies of the several enzymes involved inacetylation and deacetylation of histone residues have revealed apossible relationship between gene transcriptional activation andhistone acetylation. Since BRCA2 appear to function as a transcriptionalfactor, Histone acetyl transferase (HAT) activity of BRCA2 was tested.Also, evidence that BRCA2 has intrinsic HAT activity, which maps to theamino-terminal region of BRCA2, was presented. It was demonstrated thatBRCA2 proteins acetylate primarily H3 and H4 of free histones. Theseobservations suggest that HAT activity of BRCA2 may play an importantrole in the regulation of transcription and tumor suppressor function(Siddique et al. (1998)). These types of genes are very important forregulation of genes involved in development, cell cycle control, andchromatin structure.

At5g61520 Showing Homology to STP3 Sucrose Transporter

For developing seeds of grain legumes, photoassimilates released to theseed apoplasm from maternal seed coats are retrieved by abaxialepidermal and subepidermal cells (dermal cell complexes) of cotyledonsfollowed by symplasmic passage to their underlying storage parenchymacells. In some species, the cells of these complexes differentiate intotransfer cells (e.g. broad bean and pea, Patrick and Offler, 2001).Sucrose is a major component of the photoassimilates delivered tocotyledons (Patrick and Offler, 2001; Weber et al., 1997b).

Sucrose transporter (SUT) genes have been cloned, and functionallycharacterized as sucrose/H+ symporters, from developing cotyledons ofbroad bean (VfSUT1, Weber et al., 1997a) and pea (PsSUT1, Tegeder etal., 1999). SUTs and P-type H+-ATPases have been shown to co-localize toplasma membranes of dermal cell complexes in developing cotyledons ofbroad bean (Harrington et al., 1997; Weber et al., 1997a) and Frenchbean (Tegeder et al., 2000). In contrast, for pea cotyledons, SUT isalso present in storage parenchyma cells, but is 4-fold less active thanSUT(s) localized to epidermal transfer cells (Tegeder et al., 1999).These type of genes are Important for seed filling.

At5g66210 Showing Homology to Calcium Dependent Protein Kinase

In plants, numerous Ca(2+)-stimulated protein kinase activities occurthrough calcium-dependent protein kinases (CDPKs). These novel calciumsensors are likely to be crucial mediators of responses to diverseendogenous and environmental cues. However, the precise biologicalfunction(s) of most CDPKs remains elusive. The Arabidopsis genome ispredicted to encode 34 different CDPKs. The Arabidopsis CDPK gene familywas analyzed and the expression, regulation, and possible functions ofplant CDPKs was reviewed. By combining emerging cellular and genomictechnologies with genetic and biochemical approaches, thecharacterization of Arabidopsis CDPKs provides a valuable opportunity tounderstand the plant calcium-signaling network (Cheng et al., 2002).These type of genes are Important for stress signaling.

At2g25970 Showing Homology to KH RNA Binding Domain

Lorkovic and Barta (2002) described RNA recognition motif (RRM) and Khomology (KH) domain RNA-binding proteins from the flowering plantArabidopsis thaliana. The most widely spread motifs are the RNArecognition motif (RRM) and the K homology (KH) domain. The Arabidopsisgenome encodes 196 RRM-containing proteins, a more complex set thanfound in Caenorhabditis elegans and Drosophila melanogaster. Inaddition, the Arabidopsis genome contains 26 KH domain proteins. Most ofthe Arabidopsis RRM-containing proteins can be classified intostructural and/or functional groups, based on similarity with eitherknown metazoan or Arabidopsis proteins. Approximately 50% of ArabidopsisRRM-containing proteins do not have obvious homologues in metazoa, andfor most of those that are predicted to be orthologues of metazoanproteins, no experimental data exist to confirm this. Additionally, thefunction of most Arabidopsis RRM proteins and of all KH proteins isunknown. The higher complexity of RNA-binding proteins in Arabidopsis,as evident in groups of SR splicing factors and poly(A)-bindingproteins, may account for the observed differences in mRNA maturationbetween plants and metazoa. The function of this type of genes islargely unknown, but could be related to PUMILIO genes from Drosophila.Important for regulation of gene expression at the post-transcriptionallevel, role in development, stress tolerance.

At3g07800 Showing Homology to Thymidine Kinase

This type of thymidine kinase genes is cell cycle regulated, E2Fregulated, is responsible for production of thymidine triphosphate. Thistype of gene plays a role as a precursor for DNA synthesis and istherefore a marker of S phase.

At5g47370 Showing Homology to Homeobox Leucine Zipper Protein.

This type of homeobox genes is important for development and growth andalso for stress tolerance. At5g47370 is homeobox-leucine zipper proteinHAT2 (HD-ZIP protein 2). Homeobox genes are known as transcriptionalregulators that are involved in various aspects of developmentalprocesses in many organisms. Homeodomain transcription factors regulatefundamental body plan of plants during embryogenesis, as well asmorphogenetic events in the shoot apical meristem (SAM) afterembryogenesis. HOX1 belongs to the subset of homeodomain leucine zipper(HD-zip) and is involved in the regulation of vascular development(Scarpella et al., 2000; Meijer et al., 2000). The sequences for therice OsHOX1 orthologue are deposited in Genbank under the accessionnumber X96681 (cDNA) and CAA65456.2 (protein), which sequences are bothherein incorporated by reference.

BAA23337.1 OsMYB1

MYB-like DNA binding proteins are involved in the control of specificdevelopmental steps in different organs. OSMYB1 binds to a seed specificelement in the seed storage protein glutelin, is expressed in endospermof rice seeds, and plays an important role during seed maturation(Suzuki et al., 1997).

BAA89798 OsNAC4

NAC domain containing genes, such as NO APICAL MERISTEM in petunia andCUP-SHAPED COTYLEDON2 and NAP in Arabidopsis, have crucial functions inplant development (Kikuchi et al., 2000). These genes are involved inthe control of organ primordium delimitation and lateral organdevelopment. It has also been recently shown that a member of the NACfamily of transcription factor can induces formation of ectopic shootson cotyledons (Daimon et al., 2003).

AAD37699 Rice Homeodomain Leucine Zipper Protein HOX6 (Partial)

Homeobox genes are known as transcriptional regulators that are involvedin various aspects of developmental processes in many organisms.Homeodomain transcription factors regulate fundamental body plan ofplants during embryogenesis, as well as morphogenetic events in theshoot apical meristem (SAM) after embryogenesis. HOX6 is a homologue ofthe Arabidopsis homeobox gene Athb-12 (Lee et al., 2001). Athb-12 is atranscriptional activator important in regulating certain developmentalprocesses as well as in the plant's response to water stress involvingABA-mediated gene expression. At3g61890 is the Arabidopsis sequencecorresponding with the rice HOX6 sequence of AAD37699.

AK104073 OsMYB Predicted

This gene is homologous to the Arabidopsis gene CIRCADIAN CLOCKASSOCIATED (CCA1) gene that encodes a related MYB transcription factor,which regulates circadian rhythms (Carre et Kim, 2002). This gene aswell as the MYB homologue, regulate the period of circadian rhythms ingene expression and leaf movements.

Example 9 NMR Study of E2Fa/DPa Overexpressing Plants

In support of the microarray studies identifying the increased ordecreased expression level of E2F-target genes in E2Fa-DPaoverexpressing plants, the effects of E2Fa/DPa overexpression on theprotein level and ultimately on the level of metabolites were studiedvia the techniques of metabolomics. Metabolomics means qualitative andquantitative analysis of the metabolites present at a certain time in acell culture or a whole biological tissue. Metabolites, as designatedhere, are small molecular weight molecules (typically under 1000Daltons), of which many are already known (such as urea, lipids, glucoseor certain small hormones) while others are still to be identified.Metabolites are the final product of the protein content of the cell.The main methods used to detect and quantify of those molecules are massspectrometry or NMR spectroscopy (Nicholson et al., 2002) afterextraction and purification of the metabolites from the organism.

Now NMR spectroscopy on whole organisms has been performed. Therecording of spectra of the metabolites was possible without any priorpurification of the plant material. Hereto, the samples were spun at themagic angle. This technique, dubbed “High Resolution Magic AngleSpinning” (HRMAS) NMR, has now been used on intact plantlets. 1H-13CHSQC spectra were recorded on intact wild-type and E2Fa/DPaoverexpressing plantlets of Arabidopsis thaliana, and monitored thechanges in metabolite pattern. From the spectra, a shift in themetabolome of E2Fa/DPa overexpressing plants when compared to wild-typeplants, was observed. These spectra are processed in order to map theobserved metabolic differences.

Example 10 Molecular and Phenotypic Analysis of Arabidopisis PlantsTransformed with the Genes According to the Present Invention

Arabidopsis thaliana plants are transformed with at least one of thegenes of the present invention as presented in Table 4 or 5, operablylinked to a plant promoter.

In one example, Arabidopsis plants were transformed with the genes aspresented in Table 6. The vectors used ware derived from the expressionvector pK7WGD2, carrying the CaMV35S promoter for expression of thegene. For transformation, the flower dip method described by Bechtoldand Pelletier (1998) was used. TABLE 6 Genes that were selected andtransformed into Arabidopsis pDON CODE AGI GENE PRIMERS PCR R207 PK7WGD2Flower dip  1 At1g33960 AIG1 282 + 283  2 At1g21690 Putative replicationfactor 284 + 285 OK OK  3 At3g23250 Myb transcription factor 286 + 287 4 At5g08450 Unknown 288 + 289 OK OK OK(clone1) OK  5 At3g45730 Unknown290 + 291 OK OK OK(clone4) OK  6 At1g56150 Unknown 292 + 293  7At5g66580 Unknown 294 + 295 OK OK OK OK  8 At4g33050 Unknown 296 + 297OK OK OK OK  9 At1g76970 Unknown 298 + 299 OK partieel OK(clone4) 10At2g41780 Unknown 300 + 301 OK OK OK(clone1) OK 11 At5g14530 WD40 repeatprotein 302 + 303 OK OK OK OK A At3g02550 Unknown 310 + 311 OK OKOK(A10.7) OK B At5g47370 homeobox-leucine zipper 312 + 313 OK OKOK(clone4) OK protein-like C At1g57680 Unknown 314 + 315 OK D At1g07000leucine zipper-containing 316 + 317 OK OK OK protein E At2g22430homeodomain TF Athb-6 318 + 319 OK OK OK(clone1) OK F At4g28330 Unknown320 + 321 OK OK OK(clone4) OK G At3g23750 receptor kinase 322 + 323 OKOK H At5g66210 Ca-dep kinase 324 + 325 OK OK OK(clone2) OK I At4g02680Unknown 326 + 327 OK(clone4) OK J At2g30590 worky74 328 + 329 OK OKOK(clone2) OK K At2g46650 Unknown 330 + 331 L At2g47440 Unknown 332 +333 OK OK OK(clone5) OK M At2g15510 Unknown 334 + 335 12 At5g56740Histone acetylase HAT B 348 + 349 OK OK OK OK 13 At3g24320 Putativemismatch binding 350 + 351 OK OK OK(13, 4) OK protein 14 At4g00730Anthocyaninless2 352 + 353 15 At1g23030 arm-repeat containing protein354 + 355 OK OK OK(clone11) OK 16 At5g54380 receptor-protein kinase-like356 + 357 protein 17 At1g72180 putative leucine-rich receptor- 358 + 359OK OK OK OK like protein kinase 18 At1g61100 Unknown 360 + 361 OK OKOK(18, 1) OK 19 At2g25970 Unknown 362 + 363 OK OK OK OK 20 At2g38310Unknown 364 + 365 OK OK OK OK 21 At3g45970 Unknown 366 + 367 OK OKOK(21, 3) OKCode: internal reference code of the gene;AGI: accession number of the protein in the internal dataset, here withreference to the MIPS database accession number;Gene: name of the protein;primers: PCR primers used to isolate the ORF of the gene by RT-PCR usingcDNA;prepared form E2Fa-DPa overexpressing plants;PCR: PCR completed successfully;pDONR207: cloning in this vector completed (www.invitrogen.com);pK7WGD2: cloning of the genes in the vector under control of the CaMV35S promoter (Karimi et al., Trends Plant Sci. 2002 May; 7(5): 193-5);Flower dip: transformation of Arabidopsis plants with the pK7WGD2vector.

The transformed Arabidopsis plants are evaluated as described below.

After molecular analysis (PCR, RT-PCR, Western-blot, southern-blot,Northern blot, NMR), the plants with modified E2F target gene expressionlevels, are submitted to phenotypic analysis. Special attention is givento root growth and leaf development.

The root of A. thaliana, which has a rather constant diameter and ratheruncomplicated radial symmetry, is a perfect model system for studyingand determining the effects of modulation of expression levels of anE2F-target on an intact, growing tissue.

The root of A. thaliana comprises a thick unicellular layer of theepidermis cells, one of cortex cells, one of endodermis cells and one ofpericyclus cells that circumvent the vascular tube. Because of itstransparency, the root of A. thaliana, these cellular layers can bevisualized by interference contrast microscopy. By this means the originof the cells in a specific cell layer can be traced back to a set ofdividing mother cells in the meristem (Dolan et al., 1993). Bymeasurement of the cell length of a specific cell layer in function ofthe distance to the root tip, and the rate of movement of the cells awayfrom the root tip (measured via time-laps photography), it is possibleto determine the contribution of both the cell elongation as well as ofcell division to the total root growth (Beemster and Baskin, 1998).

The effects of the E2F-target overexpression in the leaves is determinedvia microscopic techniques after clearance of the leaves of lactic acid.This analysis is performed on the first developed leaf pear, since thisleaf pear is most comparable between different plants. By measurement ofthe cell number and the number of epidermal cells at different timepoints during leaf development, it is deduced when the leaf cells stopto divide, when they start to differentiate, the duration of their cellcycle is, and their final cell size (De Veylder et al., 2001 a and b).Moreover, this method allows the analysis of the effect of E2F targetoverexpression on the formation of stomata.

The effect of the E2F-target overexpression is also studied viabiochemical means. Functional assays are developed for the specificenzymatic activity of the studied E2F-target gene. These functionalmethods are based on expression of a reported gene in case theE2F-target is in itself a transcription activator or repressor.Functional assays are based on the incorporation of radioactive nitrogenor radioactive carbon or other radiolabelled metabolites when the enzymeis involved in the nitrogen or carbon metabolisms or other processesinvolving metabolites. By the comparison of the incorporatedradioactivity between the control line and the transgenic line, theenzymatic activity of the E2F-target can be measured.

Functional assays are based on the incorporation of radioactive ATP,radioactive purines or pyrimidines when the enzyme is involved in DNAreplication and/or modification. Functional assays are based on labeledcarbohydrates when the enzyme is involved in cell wall biogenesis, orATP when the enzyme is involved in processes of the chloroplast, orcalcium when the enzyme is involved in signal transduction.

In A. thaliana, besides the mitotic cell cycle also an alternative cellcycle is observed, in which DNA is replicated in the absence of mitosisor cytokinesis. This so-called endoreduplication process occurs often inplants. Until today, the physiological significance of endoreduplicationis unknown. Possibly, it is a mechanism to increase the number of DNAcopies per cell, which allows more transcription. In support of thishypothesis, endoreduplication often occurs in cells with high metabolicactivity (Nagl, 1976). However, as a consequence of endoreduplicationthe cells are bigger, which is especially useful for increasing yield ofcytoplasmatic component, for example storage proteins of the seed cells.

To study the effects of E2F-target overexpression on the process ofendoreduplication, the DNA content of the control plants and thetransgenic plant is measured via flow-cytometry. A more detailedanalysis is obtained by measuring the DNA content of individual cellscolored with DNA-binding fluorochrome (e.g. DAPI). The intensity of thecolor of the nucleus is in proportion with Its DNA content. RelativeDNA-measurements can be obtained via a microdensitometer. This techniqueallows determining a specific tissue the endoreduplication pattern ofthe transgenic plants.

Example 11 Use of the Invention in Corn

The invention described herein can also be used in maize. To this aim, agene according to the present invention as presented in Table 4 or 5,for example a gene selected from Tables 1 or 2, or a gene selected fromthe group described in Example 8, or a gene selected from the grouppresented in Table 6 or 7, or a homologue thereof such as for example amaize ortholog or a rice ortholog, is cloned under control of a promoteroperable in maize, in a plant transformation vector suited forAgrobacterium-mediated transformation of corn. These constructs aredesigned for overexpression or for downregulation. In a series ofexperiments, genes selected from Table 5 (downregulated in E2Fa/DPtransgenics) are overexpressed in transgenic corn and genes selectedfrom Table 4 (upregulated in E2Fa-DPa overexpressing plants) aredownregulated in transgenic corn. Suitable promoter for drivingexpression of the genes of the present invention are as presented inTables I, II, III and IV or in Table V.

Suitable promoter for driving expression of the genes of the presentinvention in corn are the rice GOS2 promoter or any other promoter asmentioned herein above. Vectors useful for expression of one or more E2Ftargets according to the present invention are standard binary vectors,such as the pPZP vector described in Hajdukiewicz et al. ((1994) PlantMol Biol 25: 989-994) or a superbinary vector. Vectors and methods touse Agrobactorium-mediated transformation of maize have been describedin literature (Ishida et al., Nat Biotechnol. 1996 June; 14(6):745-50;Frame et al., Plant Physiol. 2002 May; 129(1):13-22) and are hereinincorporated by reference. Transgenic plants made by these methods aregrown in the greenhouse for T1 seed production. Inheritability and copynumber of the transgene are checked by quantitative real-time PCR andSouthern blot analysis and expression levels of the transgene aredetermined by reverse PCR and Northern analysis. Transgenic lines withsingle copy insertions of the transgene and with varying levels oftransgene expression are selected for T2 seed production. Progeny seedsare germinated and grown in the greenhouse in conditions well adaptedfor maize (16:8 photoperiod, 26-28° C. daytime temperature and 22-24° C.nighttime temperature) as well under water-deficient,nitrogen-deficient, and excess NaCl conditions. Null segregants from thesame parental line, as well as wild type plants of the same cultivar areused as controls. The progeny plants resulting from the selfing or thecrosses are evaluated on different growth parameters, such as biomassand developmental parameters. These parameters include stem size, numberof leaves, total above ground area, leaf greenness, time to maturity,flowering time, time to flower, ear number, harvesting time. The seedsof these lines are also checked on various parameters, such as grainsize, total grain yield (number and/or weight) per plant, and grainquality (starch content, protein content and oil content). Lines thatare most significantly improved versus the controls for any of theabove-mentioned parameters are selected for further field-testing andmarker-assisted breeding, with the objective of transferring thefield-validated transgenic traits into commercial germplasm. Methods fortesting maize for growth and yield-related parameters in the field arewell established in the art, as are techniques for introgressingspecific loci (such as transgene containing loci) from one germplasminto another. Corn plants according to the present invention havechanged growth characteristics compared to the wild-type plants, such asfor example any one or more of increased biomass, increased yield,increased number and/or size of organs (including seeds), increasedharvest index, increased rate of growth and/or development (e.g.decreased cycling time, decreased time to harvest, early flowering),increased tolerance to environmental stress conditions (e.g. toleranceto salt, drought and/or cold).

Example 12 Rice Transformation with the Genes According to the PresentInvention

In a particular example of the present invention, the genes asidentified above in Tables 4 and 5, or an orthologue from another plant,for example the rice orthologue, is transformed into rice. Inparticular, the genes as presented in Tables 6 and 7, or the riceorthologues are cloned into a plant expression vector operably linked toa promoter for overexpression or downregulation of these genes.

The genes as represented in Table 7 are cloned into a plant expressionvector operably linked to a GOS2 promoter for overexpression ordownregulation. For overexpression these genes are cloned in the senseorientation and for downregulation a hairpin construct as described inWesley et al. (2001) is made. Other promoters that are used to driveexpression of these genes are other constitutive promoters, such as forexample the ubiquitin promoter or PRO170 (high mobility group protein),or PRO61 (beta expansin promoter). Also tissue specific promoters areused to drive expression of the genes of the present invention in rice,such as for example promoters specific for meristem (PRO120:metallothionein), or vegetative tissue (PRO123: protochlorophyllidreductase), PRO173: cytoplasmic malate deshydrogenase); or endosperm(PRO90: prolamin, PRO135: alpha globulin), or embryo PRO218: oleosin,PRO151: WSI18, PRO200: OSH1, PRO175: RAB21; or the whole seed (PRO58:proteinase inhibitor), or any other promoter described herein above. Thevectors used are plant transformation vector suited forAgrobacterium-mediated transformation of rice, such as for examplebinary vectors of the pCAMBIA type or super binary vectors. Such vectorsand methods for rice transformation have been described in literature byAldemita and Hodges (1996) Chan et al. (1993), Hiei et al. (1994) or inEP1198985 and which teachings herein incorporated by reference. TABLE 7genes (presented by their encoded proteins) selected for ricetransformation >CDS3435 NP_176081.1 At1g57680 (Arabidopsis) SEQ ID NO 1MPLTKLVPDAFGVVTICLVALLVLLGLLCIAYSFYFQSHVRKQGYIQLGY and 2FSGPWIIRITFILFAIWWAVGEIFRLSLLRRHRRLLSGLDLRWQENVCKWYIVSNLGFAEPCLFLTLMFLLRAPLKMESGALSGKWNRDTAGYIILYCLPMLALQLAVVLSESRLNGGSGSYVKLPHDFTRTYSRVIIDHDEVALCTYPLLSTILLGVFAAVLTAYLFWLGRQILKLVINKRLQKRVYTLIFSVSSFLPLRIVMLCLSVLTAADKIIFEALSFLAFLSLFCFCVVSICLLVYFPVSDSMALRGLRDTDDEDTAVTEERSGALLLAPNSSQTDEGLSLRGRRDSGSSTQERY VELSLFLEAEN >CDS3436BAC42858.1 At3g45730 (Arabidopsis) SEQ ID NO 3MELPSPYSSRKEESTVPPKRGRVKIMIFRDLVRSETSMAPTPRRGRIKK and 4MIAGDLVGSGKQNNYDGDGKRGG >CDS3449 BAA23337.1 OS MYB1 (Rice) SEQ ID NO 5MGRSPCCEKAHTNKGAWTKEEDQRLIAYIRAHGEGCWRSLPKAAGLL and 6RCGKSCRLRWMNYLRPDLKRGNFTDDEDELIIRLHSLLGNKWSLIAGQLPGRTDNEIKNYWNTHIKRKLLARGIDPQTHRPLLSGGDGIAASNKRHHRRRIPYPSRRRRRPRRSSPCEAAAAAAPGRLLGRRLPQQQRHNEHGGAAVPRPQPRALGRADAELAAGGDAHQRAAGLPLLPPRLPRRGGVQLSG >CD53448 BAA89798.1OsNAC4 (rice) SEQ ID NO 7 MAAAVGGSGRRDAEAELNLPPGFRFHPTDEELWHYLCRKVARQPLPand 8 VPIIAEVDLYKLDPWDLPEKALFGRKEWYFFTPRDRKYPNGSRPNRAAGRGYWKATGADKPVAPKGSARTVGIKKALVFYSGKAPRGVKTDWIMHEYRLADADRAPGGKKGSQKLDEWVLCRLYNKKNNWEKVKLEQQDVASVAAAAPRNHHHQNGEVMDAAAADTMSDSFQTHDSDIDNASAGLRHGGCGGGGFGDVAPPRNGFVTVKEDNDWFTGLNFDELQPPYMMNLQHMQMQMVNPAAPGHDGGYLQSISSPQMKMWQTILPPF >CDS3447 AAD37699.1 OS Homeodomainleucine SEQ ID NO 9 zipper protein HOX6 (rice) and 10MDGEEDSEWMMMDVGGKGGKGGGGGGAADRKKRFSEEQIKSLESMFATQTKLEPRQKLQLARELGLQPRQVAIWFQNKRARWKSKQLEREYSALRDDYDALLCSYESLKKEKLALIKQLEKLAEMLQEPRGKYGDNAGDDARSGGVAGMKKEEFVGAGGAATLYSSAEGGGTSSTEQTCSSTPWWEF ESE >CDS3446 AK104073OSMYB predicted (rice) SEQ ID NO 11MASIVTATVAAASAWWATQGLLPLFPPPIAFPFVPAPSAPFSTADVQRA and 12QEKDIDCPMDNAQKELQETRKQDNFEAMKVIVSSETDESGKGEVSLHTELKISPADKADTKPAAGAETSDVFGNKKKQDRSSCGSNTPSSSDIEADNAPENQEKANDKAKQASCSNSSAGDNNHRRFRSSASTSDSWKEVSEEGRLAFDALFSRERLPQSFSPPQVEGSKEISKEEEDEVTTVTVDLNKNAAIIDQELDTADEPRASFPNELSNLKLKSRRTGFKPYKRCSVEAKENRVPASDEVGTKRIRLESEAST >CDS3445 NP_565887.1 At2g38310 (Arabidopsis) SEQ IDNO 13 MLAVHRPSSAVSDGDSVQIPMMIASFQKRFPSLSRDSTAARFHTHEVG and 14PNQCCSAVIQEISAPISTVWSVVRRFDNPQAYKHFLKSCSVIGGDGDNVGSLRQVHVVSGLPAASSTERLDILDDERHVISFSWGGDHRLSNYRSVTTLHPSPISGTVVVESYVVDVPPGNTKEETCDFVDVIVRCNLQSLAKIAEN TAAESKKKMSL >CDS3444NP_565703.1 At2g30590WRKY SEQ ID NO 15 family transcription factor(Arabidopsis) and 16 MEEIEGTNRAAVESCHRVLNLLHRSQQQDHVGFEKNLVSETREAVIRFKRVGSLLSSSVGHARFRRAKKLQSHVSQSLLLDPCQQRTTEVPSSSSQKTPVLRSGFQELSLRQPSDSLTLGTRSFSLNSNAKAPLLQLNQQTMPPSNYPTLFPVQQQQQQQQQQQQQEQQQQQQQQQQQFHERLQAHHLHQQQQLQKHQAELMLRKCNGGISLSFDNSSCTPTMSSTRSFVSSLSIDGSVANIEGKNSFHFGVPSSTDQNSLHSKRKCPLKGDEHGSLKCGSSSRCHCAKKRKHRVRRSIRVPAISNKVADIPPDDYSWRKYGQKPIKGSPYPRGYYKCSSMRGCPARKHVERCLEDPAMLIVTYEAEHNHPKLPSQAITT >CDS3443 NP_849867.1At1g69510 (Arabidopsis) SEQ ID NO 17MEDVKGKEIIDDAPIDNKVSDEMESEENAIKKKYGGLLPKKIPLISKDHE and 18RAFFDSADWALGKQKGQKPKGPLEALRPKLQPTPQQQPRARRMAYSSGETEDTEIDNNEAPDDQACASAVDSTNLKDDGGAKDNIKS >CDS3442 NP_564615.3 At1g52870(Arabidopsis) SEQ ID NO 19MAAASLHTSISPRSFLPLSKPSLKPHRSQILLRNKQRNCVSCALIRDEID and 20LIPVQSRDRTDHEEGSVVVMSTETAVDGNESVVVGFSAATSEGQLSLEGFPSSSSSGADLGDEKRRENEEMEKMIDRTINATIVLAAGSYAITKLLTIDHDYWHGWTLFEILRYAPQHNWIAYEEALKQNPVLAKMVISGVVYSVGDWIAQCYEGKPLFEIDRARTLRSGLVGFTLHGSLSHFYYQFCEELFPFQDWWVVPVKVAFDQTVWSAIWNSIYFTVLGFLRFESPISIFKELKATFLPMLTAGWKLWPFAHLITYGLVPVEQRLLWVDCVELIWVTILSTYSNEKSEARISESVIETSSSSTTTIDPSKE >CDS3441 NP_849293.1 At4g02920 (Arabidopsis) SEQID NO 21 MIKLCFMTSHGYSIPGLGLPQDLCNTEIIKQNSRSHLVNPGARQEIIPAS and 22SFNLNTELLEPWKPVSSFSQFVEIDSAMMKPLLMDVHETAPESLILSFGIADKFARQEKVMEFLLSQSEEFKEKGFDMSLLNELMEFESMKSSSQLRPYDTSSVLYLNQELGKPVLDLVRDMMENPEFSVRSNGHVLFSSSSNPELNDLLSIASEFNLSRNSTTKWRQLSPLIPHFQRFESDVFTPAKLKAVTVLAPLKSPEKSRLKSPRKHNTKRKAKERDLYKRNHLHAYESLLSLMIGNDHRHKHTTVLSLQKSCGELSELLTQFSITAAGTGIAVLFSVVCSLASRRVPFCANKFFDTGLGLSLVILSWAVNRLREVIVHVNRKANKPCSSLKDDEIINSVERSMKEVYYRAATVIAVFALRFAC >CDS3440 AAM91100.1 At1g45200 (Arabidopsis)SEQ ID NO 23 MSKTNMKFCNSYFLVDPTKASFLDLLLLLFSSNLTSARFIDSPPDTLKGF and 24RRSFASRWILALAIFLQKVLMLLSKPFAFIGQKLTYWLNLLTANGGFFNLILNLMSGKLVKPDKSSATYTSFIGCSDRRIELDEKINVGSIEYKSMLSIMASKISYESKPYITSVVKNTWKMDLVGNYDFYNAFQESKLTQAFVFKTSSTNPDLIVVSFRGTEPFEAADWCTDLDLSWYEMKNVGKVHAGFSRALGLQKDGWPKENISLLHQYAYYTIRQMLRDKLGRNKNLKYILTGHSLGGALAALEPAILAIHGEDELLDKLEGIYTFGQPRVGDEDFGEFMKGVVKKHGIEYERFVYNNDVVPRVPFDDKYLFSYKHYGPCNSFNSLYKGKVREDAPNANYFNLLWLIPQLLTGLWEFIRSFILQFWKGDEYKENWLMRFVRWGIVFPGGSNHFPFDYVNSTRLGGLVRPPPTTTPEDKLALIA

Transgenic plants generated by these rice transformation methods areevaluated for various growth characteristics. More particularly, thetransgenic plants are evaluated and the following parameters aremonitored: increased total above ground biomass, increased plant height,increased number of tillers, increased number of first panicles,increased number of second panicles, increased total number of seeds,increased number of filled seeds, increased total seed yield (weigth)per plant, increased harvest index, increased thousand kernel weight,increased Tmid, increased T45 or A90, increased A42, changed cyclingtime or an changed growth curve, changed flowering time.

Plants with increase biomass, increased organ number and/or size(including seeds) and or any other economically attractive growthcharacteristics as found by the following plant evaluation protocol, areselected to transferring the transgenic traits into commercialgermplasm.

Evaluation Protocol for T0, T1 and T2 Transgenic Rice Plants Transformedwith an E2F Target Gene According to the Present Invention

Approximately 15 to 20 independent T0 rice transformants are generated.The primary transformants are transferred from tissue culture chambersto a greenhouse for growing and harvest of T1 seed. Approximately 6events, of which the T1 progeny segregated 3:1 for presence/absence ofthe transgene, are retained. For each of these events, approximately 10T1 seedlings containing the transgene (hetero- and homo-zygotes), andapproximately 10 T1 seedlings lacking the transgene (nullizygotes), areselected by monitoring screenable marker expression.

2 events with improved agronomical parameters in T1 are chosen forre-evaluation in T2 generation. Seed batches from the positive plants(both hetero- and homozygotes) in T1, are screened by monitoring markerexpression. For each chosen event, the heterozygote seed batches arethen selected for T2 evaluation. An equal number of positives andnegatives within each seed batch are transplanted for evaluation in thegreenhouse. The total number of 120 transformed plants is evaluated inthe T2 generation. More particularly, two transformed events areselected, 60 plants per event of which 30 positives for the transgene,and 30 negative.

T1 and T2 plants are transferred to the greenhouse and evaluated forvegetative growth parameters and seed parameters, as describedhereunder.

Statistical Analysis: t-test and F-test

A two factor ANOVA (analysis of variants) is used as statistical modelfor the overall evaluation of plant phenotypic characteristics. AnF-test is carried out on all the parameters measured, for all of theplants of all of the events transformed with the gene of interest. TheF-test is carried out to check for an effect of the gene over all thetransformation events and to determine the overall effect of the gene or“global gene effect”. Significant data, as determined by the value ofthe F-test, indicates a “gene” effect, meaning that the phenotypeobserved is caused by more than the presence or position of the gene. Inthe case of the F-test, the threshold for significance for a global geneeffect is set at a 5% probability level.

To check for an effect of the gene within an event, i.e., for aline-specific effect, a t-test is performed within each event using datasets from the transgenic plants and the corresponding null plants. “Nullplants” or “Null segregants” are the plants treated in the same way asthe transgenic plant, but from which the transgene has segregated. Nullplants can also be described as the homozygous negative transformants.The threshold for significance for the t-test is set at 10% probabilitylevel. Within one population of transformation events, some events canbe under or above this t-test threshold. This is based on the hypothesisthat a gene might only have an effect in certain positions in thegenome, and that the occurrence of this position-dependent effect is notuncommon. This kind of gene effect may also be referred to as a “lineeffect of a gene”. The p-value is obtained by comparing the t-value tothe t-distribution or alternatively, by comparing the F-value to theF-distribution. The p-value stands for the probability that the nullhypothesis (null hypothesis being “there is no effect of the transgene”)is correct.

Vegetative Growth Measurements:

The selected transgenic plants are grown in a greenhouse. Each plantreceives a unique barcode label to link unambiguously the phenotypingdata to the corresponding plant. The selected transgenic plants aregrown on soil in 10 cm diameter pots under the following environmentalsettings: photoperiod=11.5 h, daylight intensity=30,000 lux or more,daytime temperature=28° C. or higher, night time temperature=22° C.,relative humidity=60-70%. Transgenic plants and the correspondingnullizygotes were grown side-by-side at random positions. From the stageof sowing until the stage of maturity each plant is passed several timesthrough a digital imaging cabinet and imaged. At each time point digitalimages (2048×1536 pixels, 16 million colours) are taken of each plantfrom at least 6 different angles. The parameters described below arederived in an automated way from all the digital images of all theplants, using image analysis software.

(a) Above ground plant area is determined by counting the total numberof pixels from aboveground plant parts discriminated from thebackground. This value is averaged for the pictures taken on the sametime point from the different angles and converted to a physical surfacevalue expressed in square mm by calibration. Experiments show that theaboveground plant area measured this way correlates with the biomass ofplant parts above ground.

(b) Plant height is determined by the distance between the horizontallines going through the upper pot edge and the uppermost pixelcorresponding to a plant part above ground. This value is averaged forthe pictures taken on the same time point from the different angles andwas converted, by calibration, to a physical distance expressed in mm.Experiments showed that plant height measured this way correlate withplant height measured manually with a ruler.

(C) Number of primary tillers is manually counted at the harvesting ofthe plants. The tillers are cut off at 3 cm above the pot rim. They werethen counted at the cut surface. Tillers that were together in the samesheet were counted as one tiller.

(d) Number of primary panicles. The tallest panicle and all the paniclesthat overlap with the tallest panicles when aligned vertically arecounted manually, and considered as primary panicles.

(e) Number of secondary panicles. The number of panicles that remainedon the plant after the harvest of the primary panicles are counted andconsidered as secondary panicles.

(f) Growth curve. The plant area weekly measurements are modeled toobtain a growth curve for each plant, plotted as the value of plant area(in mm²) over the time (in days). From this growth curve the followingparameters are calculated.

(g) A42 is the plant area at day 42 after sowing as predicted by thegrowth curve model.

(h) Tmid is the time that a plant needs to grow and to reach 50% of themaximum plant area. Tmid is predicted from the growth curve model.

(i) T90 is the time that a plant needs to grow and to reach 90% of themaximum plant area. T90 is predicted from the growth curve model.

Seed-Related Parameter Measurements

The mature primary panicles of T1 and T2 plants are harvested, bagged,barcode-labelled and then dried for three days in the oven at 37° C. Thepanicles are then threshed and all the seeds were collected and counted.The filled husks are separated from the empty ones using an air-blowingdevice. The empty husks are discarded and the remaining fraction iscounted again. The filled husks are weighed on an analytical balance.This procedure resulted in the set of seed-related parameters describedbelow.

(a) Total seed number per plant is measured by counting the number ofhusks harvested from a plant.

(b) Number of filled seeds is determined by counting the number offilled husks that remained after the separation step.

(c) Total seed yield per plant is measured by weighing all filled husksharvested from a plant.

(d) Harvest index of plants is defined as the ratio between the totalseed yield and the above ground area (mm²), multiplied by a factor 10⁶.

(e) Thousand Kernel Weight (TKW) of plants is a parameter extrapolatedfrom the number of filled seeds counted, and their total weight.

(f) Total Area Emergence Prop. is the time when plant reach 30% of theirmaximum total area

(g) Total Area Cycle Time. is the time when plant reach 90% of theirmaximum total area

Further molecular analysis is performed on the positive plants bytechniques well known by the person skilled in the art such as forexample RT-PCR.

Tables TABLE 1 Arabidopsis Genes 2-fold or more upregulated in E2Fa/DPaplants OLD REF SEQ ID NO Gene Identification accession # MIPS name cDNAPROT cDNA PROT Fold induction E2F site Plant homologue Unknown function(14) hypothetical protein AI998042 At1g57680 1 53 433 434 2.66 riceBAB90159.1, maize AY107220.1 putative protein AI994686 At3g45730 2 54231 232 5.14 putative protein AI994734 At5g66580 4 56 489 490 3.18unknown protein AI999397 At2g38310 5 57 995 996 2.79 TTTGCCCC riceBAB68102.1 unknown protein AI995465 At2g47440 7 59 931 932 2.50 unknownprotein AI994871 At1g76970 8 60 1193 1194 2.34 rice BAB78689.1, cornAAB00079.1 hypothetical protein, AI998366 At1g27500 9 61 393 394 2.21rice AAL87057.1 kinesin putative protein AI996967 At4g33050 10 62 883884 2.20 rice BAB90008.1 putative protein AI995917 At3g43690 12 64 263264 2.18 unknown protein, kh AI993084 At2g25970 13 65 941 942 2.15 riceBAA92910.1, domain protein maize AY106526.1 unknown protein AI993077At1g68580 14 66 937 938 2.13 rice BAC00723.1, corn AAK11516.1 putativeprotein, copine AI993019 At5g14420 15 67 205 206 2.05 rice BAB92575.1hypothetical protein AI997428 At1g57990 16 68 415 416 2.02 riceBAB90042.1 unknown protein AI997827 At5g53740 17 69 2731 2732 2.01 DNAreplication and modification (14) putative thymidine AI997851 At3g078008.44 rice AAC31168.1 kinase DNA methyltransferase AI994691 At5g491605.37 ATTGCCGC rice AAL77415.1, corn AAC16389.1 Msi3 AW004204 At4g350504.89 TTTCCCGC corn AAL33648.1 putative linker histone AI994590 At3g180353.31 protein putative replication AI997934 At1g21690 3.30 TTTCCCGCfactor c topoisomerase 6 AI995290 At5g02820 2.62 TTTCCCGC subunit Ahistone H4-like protein AI999171 At3g46320 2.55 TTTGGCGC histoneacetylase HAT B AI998229 At5g56740 2.36 TTTCCCGC corn AAM28228.1putative histon H1 AI996137 At1g06760 2.27 histone H2A-like proteinAI995882 At4g27230 2.23 putative DNA gyrase AI995400 At3g10690 2.20 riceAAD29710.1 subunit A histone H2B-like protein AI999101 At5g59910 2.16putative mismatch AI993280 At3g24320 2.10 rice CAD41187.1, bindingprotein corn AAF35250.1 adenosylhomocysteinase AI996953 At4g13940 2.07corn AAL33588.1 Cell Cycle (2) E2Fa AJ294534 At2g36010 94.88 CDKB1; 1D10851 At3g54180 2.60 TTTCCCGC Cell wall biogenesis (11) xyloglucanendo-1;4- AI994459 At4g30270 3.74 beta-D-glucanase (meri- 5) putativeglycosyl AI999244 At1g70090 3.38 transferase alpha AI998223 At3g627203.26 galactosyltransferase- like protein putative xyloglucan AI999683At3g23730 2.85 rice CAD41426.1, endotransglycosylase corn CAB510059.1xyloglucan endo-1,4- AI998301 At4g30280 2.74 beta-D-glucanase-likeprotein putative xyloglucan AI994477 At1g14720 2.51 endotransglycosylaseputative glycosyl AI999770 At1g24170 2.39 transferase putativeUDP-glucose AI997288 At1g22400 2.34 TTTCCCGC glucosyltransferaseputative AI998872 At2g15480 2.15 glucosyltransferase peroxidase AI994622At2g38380 2.11 TTTCGCCC beta-1,3-glucanase-like AI994681 At3g55430 2.05rice AAB37697.1, protein corn CAB96424.1 Chloroplastic genes (7) largesubunit of N96785 rbcL 2713 2714 4.71 NP_051067 ribulose-1,5-bisphosphate carboxylase/oxygenase ribosomal protein L33 AI994194 rpl332715 2716 3.54 NP_051080 PSII I protein AW004203 psbl 2717 2718 2.81NP_051074 ribosomal protein L2 AW004266 rpl2 2719 2720 2.61 NP_051099ATP-dependent AI997947 clpP 2721 2722 2.60 NP_051083 protease subunitcytochrome B6 AI997102 petB 2723 2724 2.55 NP_051088 ATPase epsilonsubunit AW004251 atpE 2725 2726 2.17 NP_051065 Mitochondrial genes (1)26S ribosomal RNA AW004275 orf107a 2727 2728 2.87 NP_085475 proteinTranscription factors (6) LOB domain protien 41 AI996685 At3g02550 3 551109 1110 4.01 riceBAB92193.1 WRKY transcription AI992739 At2g30590 2.78TTTCCCCC factor 21 GATA Zn-finger protein AI995731 At3g16870 6 58 27292730 2.75 maize AY072149 Anthocyaninless2 AI993655 At4g00730 2.73TTTCCCCC leucine zipper- AI995691 At1g07000 2.43 containing proteinhomeodomain AI999190 At2g22430 2.30 rice CAA65456.2, transcriptionfactor corn CAB96424.1 (Athb-6) Metabolism and biogenesis (11) alcoholdehydrogenase AI998773 At1g77120 5.09 putative isocistrate AI999168At3g21720 3.08 lyase protochlorophyllide AI993342 At4g27440 2.39reductase precursor suger transpoter like AI997793 At4g36670 2.27 riceAAK13147.1, protein corn AAF74568.1 NADH-dependent AI997600 At5g534602.25 glutamate synthase (GOGAT) nitrate reductase (NIA2) AI996208At1g37130 2.15 pectate lyase - like AJ508995 At3g54920 2.13 proteinputative sterol AI996340 At2g43420 2.10 dehydrogenase glutaminesynthetase 161G19T7 At1g66200 2.06 root isozyme 1 (GS) monosaccharideAI997045 At5g61520 2.05 rice BAA83554.1, transporter STP3 cornAAF74568.1 Signal transduction (6) calcium-dependent AI996555 At5g662102.96 rice AAF23901.2, protein kinase corn BAA12715.1 WD-40 repeatprotein AI993055 At5g14530 2.70 rice AD27557.1, corn AAA50446.1receptor-protien kinase- AI994727 At5g54380 2.59 rice AAK63934.1, likeprotein corn AAB09771.1 putative phytochrome A AI998146 At1g09570 2.45putative leucine-rich AI999651 At1g72180 2.13 rice BAC06203.1,receptor-like protein corn CAC35411.1 kinase putative receptor-likeAI993298 At3g23750 2.06 rice CAA69028.1, kinase corn CAC35412.1 Others(13) putative pollen allergen AI996548 At3g45970 3.22 rice AAG13596.1,corn CAD40849.1 cold-regulated protein AW004198 At5g15970 3.03 COR6,6phi-1-like protein AI994601 At5g64260 2.60 lipid-transfer protein-likeAI998609 At5g01870 2.33 rice BAB86497.1, corn AAB06443.1 DnaJ homologueAI994551 At5g06910 2.32 ATTGGCGC blue copper binding AI996535 At5g202302.30 protein src-2 like protein AI998679 At1g09070 11 63 401 402 2.19RING finger protein AI999491 At3g61460 2.14 rice BAA85438.1, cornAAL59234.1 putative Ticc22 AI993361 At3g23710 2.14 nodulin-like proteinAI996322 At1g80530 2.07 rice AAM01022.1 putative resistance AI997549At1g61100 2.06 rice AAL83695.1, protein seed imbitition protein-AI993446 At5g20250 2.05 like putative disease AI998978 At1g72900 2.04rice AAL01163.1, resistance protein corn AAC83564.1

TABLE 2 Arabidopsis Genes 2-fold or more repressed in E2Fa/DPa plantsOLD REF SEQ ID NO Fold Gene Identification accession # MIPS cDNA PROTcDNA PROT repression E2F site plant hom ologue Unknown function (35)unknown protein AI993767 At1g45200* 18 70 2741 2742 3.91 putativeprotein AI993468 At3g56290 19 71 1483 1484 3.38 maize AY106321.1, riceBAB93184.1 hypothetical protein, AI996374 At1g61890 21 73 2599 2600 2.78multidrug efflux protein unknown protein AI994573 At3g15950 22 74 21472148 2.71 putative protein AI994726 At3g52360 23 75 1619 1620 2.65hypothetical protein AI997393 At4g02920 24 76 1521 1522 2.60 TTTGCCCCY09602. Hordeum vulgare unknown protein, put AJ508997 At5g43580 25 772743 2744 2.58 protease inhibitor unknown protein AI997866 At1g70760 2678 2077 2078 2.52 unknown protein AI997085 At5g43750 27 79 1423 14242.51 rice BAB90754.1 putative protein AI995724 At5g50100** 28 80 19731974 2.48 rice AL606619.2 OSJN00032 genomic unknown protein AI995337At1g74880 29 81 2699 2700 2.42 maize AY105515.1, rice BAB89011.1 unknownprotein AI998296 At3g19370 30 82 1859 1860 2.40 unknown protein, ATPaseAI993346 At3g10420 31 83 2249 2250 2.40 putative protein AI999485At3g61080 32 84 1863 1864 2.38 unknown protein AI996923 At1g67860 33 851847 1848 2.38 unknown protein AI994841 At1g52870 34 86 2367 2638 2.35ATTCCCCC maize AY108423.1 unknown protein AI999581 At1g64370 35 87 20992100 2.35 unknown protein AI997584 At1g05870 36 88 1955 1956 2.25 riceBAB86085.1, maize Y110580.1 putative protein AI992938 At5g03540 37 892745 2746 2.21 hypothetical protein AI997712 At2g15020 38 90 2605 26062.21 rice BAB64794.1 unknown protein AI998338 At1g68440 39 91 2625 26262.20 unknown protein AI996872 At2g21960 40 92 1715 1716 2.19 putativeprotein, centrin AI996295 At4g27280 41 93 2039 2040 2.18 putativeprotein AI995642 At3g48200 42 94 2653 2654 2.16 unknown protein AI997470At2g32870 43 95 1941 1942 2.14 hypothetical protein AI998460 At1g6951044 96 2019 2020 2.11 TTTGGCCC rice BAB18340.1, maize AY110240.1 putativetriacylglycerol AI993356 At5g22460 45 97 2349 2350 2.10 lipase putativeprotein AI995956 At5g52060 46 98 1779 1780 2.08 unknown protein AI996100At2g35830 47 99 2471 2472 2.06 hypothetical protein AI996039 At3g2705048 100 2175 2176 2.05 unknown protein AI996020 At5g51720 49 101 20332034 2.04 putative protein AW004101 At4g39730 51 103 1605 1606 2.03hypothetical protein AI998372 At2g01260 52 104 1979 1980 2.03 unknownprotein AI999573 At3g61060 2.00 unknown protein AI998562 At2g35760 2.00No hit (2) no hit on genome AI995690 2.54 no hit on genome AI999010 2.23Cell wall biogenesis (4) similar to AI993509 At1g10640 50 102 1761 17623.62 maize AY106712.1, polygalacturonase-like rice BAC06884.1 proteinputative xyloglucan endo- AI997647 At2g36870 2.51 transglycosylasepectate lyase 1-like AI994801 At1g67750 2.40 protein xyloglucan endo-AI998832 At3g44990 2.35 transglycosylase Metabolism and biogenesis (24)fructose-biphosphate AI994456 At4g26530 5.99 ATTGGCCC aldolase-likeprotein sucrose-phosphate AI995432 At4g10120 4.64 synthase-like proteinputative branched-chain AI997263 At3g19710 3.31 amino acidaminotransferase vitamine c-2 AI997404 At4g26850 20 72 2511 2512 3.04TTTGCCGC maize AY105327, rice BAB90526.1 nicotianamine synthase AI993200At5g04950 2.86 beta-fructosidase AI994670 At1g62660 2.66 TTTCCCCCneoxanthin cleavage AI997269 At4g19170 2.66 enzyme-like protein putativestarch synthase AI997174 At1g32900 2.63 cytochrome P450 AI994017At4g13770 2.57 monooxygenase (CYP83A1) beta-amylase-like proteinAI999322 At5g18670 2.53 FRO1-like protein; AI995987 At5g49740 2.46 NADPHoxidase-like putative hydrolase AI997149 At3g48420 2.39 furamatehydratase AI997067 At5g50950 2.31 TTTGGCCC 5′-adenylylsulfate AI992757At1g62180 2.30 TTTCCCCC reductase 5′-adenylylsulfate AI996614 At4g046102.30 reductase UDP rhamnose- AI996803 At4g27560 2.24 anthocyanidin-3-glucoside rhamnosyltransferase - like protein cytochrome P450-likeAI993171 At5g48000 2.23 protein lactoylglutathione lyase- AI994552At1g11840 2.20 like protein putative beta-glucosidase AI995306 At4g278202.20 ATTGGCCC adenine phospho- AI994567 At4g22570 2.18ribosyltransferase-like protein catalase AI995830 At4g35090 2.17ATTCCCCC putative glutathione AW004143 At2g25080 2.15 peroxidaseputative adenosine AW004219 At2g14750 2.13 phosphosulfate kinasetyrosine transaminase AI996914 At4g23600 2.13 like protein Transcriptionfactors (5) homeobox-leucine zipper AI994027 At3g61890 4.20 proteinATHB-12 NAC domain protein AI992865 At1g69490 3.68 NAC2 myb-relatedtranscription AI995298 At1g71030 2.78 factor dof zinc finger proteinAI994875 At1g51700 2.30 MYB-related transcription AI992931 At2g468302.19 factor (CCA1) Signal transduction (9) serine/threonine proteinAI995557 At5g10930 3.91 kinase-like protein subtilisin proteinase-likeAI993428 At4g21650 3.19 putative oligopeptide AI996160 At4g10770 2.68transporter putative lectin AI998542 At3g16400 2.52 Ca2+dependentAI998553 At1g35720 2.45 membrane-binding protein annexin putative WDrepeat AI997238 At3g15880 2.38 protein putative lectin AI999016At3g16390 2.35 putative lectin AI993358 At3g16530 2.31 SNF1 relatedprotein AI993111 At3g23000 2.06 kinase (ATSRPK1) Others (25) putativeprotease inhibitor AI995265 At1g73330 10.30 Dr4 major latex proteinAI998305 At2g01520 4.27 homolog - like pollen allergen-like AI993041At1g24020 3.56 protein putative heat shock AI997846 At1g06460 3.55protein putative fibrillin AI997199 At4g04020 3.55 major latex proteinAI997255 At1g70890 3.50 homolog - like putative nematode- AI993740At2g40000 2.95 resistance protein putative auxin-regulated AJ508998At2g46690 2.86 protein putative myrosinase- AI997583 At2g39310 2.61binding protein ubiquitin-conjugating AI997782 At5g56150 2.41enzyme-like protein ubiquitin-conjugating AI994771 At5g41700 2.40 enzymeE2-17 kD 8 vegetative storage AI999152 At5g24770 2.35 protein Vsp2 heatshock protein 70 AI994044 At3g12580 2.24 chloroplast outer AI997015At3g63160 2.20 envelope membrane protein translation initiation AI992786At5g54940 2.15 factor-like protein pseudogene AI995323 At2g04110 2.07vegetative storage AI999546 At5g24780 2.06 protein Vsp1 dehydrin ERD10AI997518 At1g20450 2.06 MTN3-like protein AI997159 At3g48740 2.05putative chlorophyll A-B AI994859 At3g27690 2.05 binding proteinphotosystem I reaction AI997939 At5g64040 2.03 centre subunit psaNAR781, similar to yeast AI998194 At2g26530 2.03 pheromone receptorputative lipid transfer AI997024 At2g15050 2.03 protein peroxidase ATP3aAI998372 At5g64100 2.03 myosin heavy chain-like AI999224 At3g16000 2.01protein*this sequence is present in the MIPs database version of Jul. 25, 2002**this record has an updated MIPS accession number At5g50101.

TABLE 3 Number of E2F elements in the different datasets UpregulatedDownregulated All genes (4518) genes (88) genes (105) TTTCCCCC 62 2 3TTTCCCGC 40 6 0 TTTCGCCC 15 0 0 TTTCGCCC 13 1 0 TTTGCCCC 37 1 1 TTTGCCGC20 0 1 TTTGGCCC 55 0 2 TTTGGCGC 15 1 0 ATTCCCCC 10 0 2 ATTCCCGC 6 0 0ATTCGCCC 8 0 0 ATTCGCCC 14 0 0 ATTGCCCC 13 0 0 ATTGCCGC 10 1 0 ATTGGCCC44 0 2 ATTGGCGC 9 1 0 Total 371  13  11

TABLE 4 Arabidopsis genes 1.3 fold or more upregulated in E2Fa/Dpaplants SEQ ID NO cDNA PROT Gene name e_value MIPS accession number ratio25 26 putative protein 0 At5g51100 1.42 27 28 endo-1,4-beta-glucanase9E−27 At1g70710 1.85 29 30 mitochondrial elongation factor Tu 1E−125At4g02930 1.39 31 32 glycine-rich protein (clone AtGRP8) 1E−155At4g39260 1.33 33 34 UTP-glucose glucosyltransferase 0 At5g66690 1.59 3536 lipid-transfer protein-like 0 At5g01870 2.33 37 38 putativeauxin-regulated protein 6E−68 At4g34760 1.48 39 40 histone H1, putative0 At1g06760 2.27 41 42 APETALA2 protein 0 At4g36920 1.44 43 44 putativehistone H2A 0 At1g08880 1.84 45 46 monosaccharide transporter STP3 2E−69At5g61520 2.05 47 48 receptor-protein kinase-like protein 8E−64At3g51550 1.33 49 50 SET-domain protein-like 1E−140 At5g04940 1.38 51 52homeodomain transcription factor (ATHB-6) 0 At2g22430 2.3 53 54 putativeprotein 0 At4g33700 1.85 55 56 hypothetical protein 1E−139 At1g058001.34 57 58 unknown protein 0 At1g33410 1.37 59 60 hypothetical protein1E−140 At4g17060 1.41 61 62 putative protein 0 At5g19820 1.44 63 64putative protein 1E+00 At3g53670 1.54 65 66 regulatory subunit ofprotein kinase CK2 0 At3g60250 1.51 67 68 delta 9 desaturase, putative 0At1g06090 1.85 69 70 putative protein 0 At5g06360 1.48 71 72 acetyl-CoAcarboxylase, putative, 5′ partial 0 At1g36170*** 1.49 73 74 hypotheticalprotein 0 At1g56150 1.97 75 76 seed imbitition protein-like 0 At5g202502.05 77 78 unknown protein 1E−146 At1g76010 1.64 79 80 homeobox-leucinezipper protein-like 0 At5g47370 2.21 81 82 kinesin-like protein 0At5g54670 1.69 83 84 putative protein 0 At3g48050 1.75 85 86 putativeprotein 0 At5g03040 1.34 87 88 xyloglucan endo-1,4-beta-D-glucanaseprecursor 0 At4g30270 3.74 89 90 putative WD-40 repeat protein 0At2g19540 1.75 91 92 putative protein 1E−132 At3g54480 1.44 93 94hypothetical protein 0 At1g15750 1.7 95 96 hypothetical protein 0At1g66200 2.06 97 98 putative protein 0 At3g50630 1.4 99 100 unknownprotein 0 At2g30930 1.3 101 102 putative protein 6E−91 At5g37720 1.8 103104 unknown protein 1E−146 At5g54310 1.61 105 106 hypothetical protein 0At1g48920 1.98 107 108 hypothetical protein 0 At1g17750 1.38 109 110nuclear RNA binding protein A-like protein 0 At4g17520 1.43 111 112unknown protein 4E+00 At1g10890 1.38 113 114 histone H2A-like protein 0At4g27230 2.23 115 116 phytochelatin synthase (gb|AAD41794.1) 0At5g44070 1.39 117 118 RNA-binding protein cp29 protein 1E−159 At3g534601.54 119 120 putative' RNA-binding protein 0 At3g25150 1.48 121 122alcohol dehydrogenase 2E−01 At5g42250 1.34 123 124 putative 60Sribosomal protein L6 1E−170 At1g74060 1.37 125 126 calmodulin-bindingprotein 1E−114 At5g57580 1.4 127 128 putative protein 3E−23 At4g203102.01 129 130 putative protein kinase 0 At1g08720 1.33 131 132hypothetical protein 0 At3g12200 1.34 133 134 putativephosphatidylserine decarboxylase 0 At4g25970 1.38 135 136 unknownprotein 0 At2g03120 1.31 137 138 unknown protein 0 At1g14880 1.48 139140 histone H2A.F/Z 0 At3g54560 1.85 141 142 4-coumarate-CoA ligase -like 0 At4g19010 1.35 143 144 putative protein 0 At3g45040 1.72 145 146unknown protein 0 At3g19540 1.84 147 148 putative protein 0 At4g344101.36 149 150 unknown protein 0 At1g61260 1.97 151 152 putative protein 0At3g61490 1.32 153 154 lipoxygenase 0 At1g17420 1.34 155 156 putativeSecA-type chloroplast protein transport factor 0 At4g01800 1.38 157 158putative DNA-binding protein 0 At4g01250 1.49 159 160 hypotheticalprotein 0 At1g20580 1.37 161 162 hypothetical protein 2E−90 At1g475301.39 163 164 unknown protein 0 At2g37570 1.84 165 166 bZIP transcriptionfactor-like protein 0 At3g62420 1.32 167 168 putative protein 1E−154At3g56720 1.39 169 170 hypothetical protein 0 At1g76860 1.32 171 1726-phosphogluconate dehydrogenase 2E−80 At5g41670 1.48 173 174 ferritin 1precursor 0 At5g01600 1.38 175 176 putative ABC transporter 0 At1g713301.71 177 178 hypothetical protein 0 At1g27300 1.3 179 180 myrosinaseprecursor 9E−01 At5g26000 2.81 181 182 unknown protein 0E+00 At1g102701.47 183 184 putative protein 3E−88 At5g18650 1.33 185 186 hypotheticalprotein 6E−40 At2g36090 1.32 187 188 unknown protein 0 At1g43910 1.42189 190 hypothetical protein 0 At1g07000 2.43 191 192 hypotheticalprotein 0 At1g18260 1.43 193 194 putative pre-mRNA splicing factor 0At4g03430 1.49 195 196 putative protein 0 At5g11810 1.32 197 198hypothetical protein 1E−151 At4g30150 1.41 199 200 S-receptor kinase -like protein 0 At4g32300 1.52 201 202 disease resistance RPP5 likeprotein 1E−175 At4g16950 1.64 203 204 unknown protein 2E−58 At1g765201.44 205 206 putative protein 1E−144 At5g14420 2.05 207 208 putativeglucosyltransferase 4E−78 At1g23480 1.31 209 210 putative protein 1E−144At4g28470 1.34 211 212 putative protein 0 At4g29830 1.55 213 214putative auxin-regulated protein 0 At2g33830 1.41 215 216 putativeprotein 8E+00 At5g61550 1.38 217 218 unknown protein 0 At1g44810 1.39219 220 protein phosphatase - like protein 1E−59 At5g02760 1.76 221 222hypothetical protein 2E−21 At4g17800 1.59 223 224 hypothetical protein 0At1g54080 1.58 225 226 xyloglucan endo-transglycosylase, putative 0At1g14720 2.51 227 228 putative protein 0 At3g49320 1.7 229 230beta-1,3-glucanase - like protein 0 At3g55430 2.05 231 232 putativeprotein 0 At3g45730 5.14 233 234 ubiquitin-conjugating enzyme E2-21 kD 1(ubiquitin-protein 0 At5g41340 1.32 ligase) 235 236 putative reticulineoxidase-like protein 0 At1g30720 1.31 237 238 DNA(cytosine-5)-methyltransferase (DNA methyltransferase) 0 At5g49160 5.37(DNA 239 240 putative protein 0 At4g32030 1.38 241 242 unknown protein3E+00 At2g32710 1.46 243 244 E2F transcription factor-1 E2F1 1E−155At5g22220 1.52 245 246 putative protein 0 At5g48820 1.8 247 248 putativeE2F5 family transcription factor 1E−154 At2g36010 94.9 249 250 proteinkinase cdc2 homolog B 0 At3g54180 2.6 251 252 putative WRKY DNA-bindingprotein 1E−164 At2g03340 1.43 253 254 hypothetical protein 0 At4g136701.56 255 256 xyloglucan endo-1,4-beta-D-glucanase-like protein 0At4g30280 2.74 257 258 hypothetical protein 1E−121 At1g18630 1.41 259260 putative protein 0 At5g35735 1.52 261 262 putative protein kinase 0At2g47060 1.32 263 264 putative protein 1E−01 At3g43690 2.18 265 266 70kD heat shock protein 0 At2g32120 1.57 267 268 nitrate reductase 0At1g37130 2.15 269 270 beta-amylase 0 At5g55700 1.55 271 272multicatalytic endopeptidase complex alpha chain 0 At3g51260 1.57 273274 putative protein 3E−02 At5g36190 2.55 275 276 putative protein 0At4g00830 1.39 277 278 monodehydroascorbate reductase (NADH) - likeprotein 0 At5g03630 1.33 279 280 unknown protein 1E−107 At3g04350 1.42281 282 hypothetical protein 0 At1g70090 3.38 283 284 E2ubiquitin-conjugating-like enzyme Ahus5 0 At3g57870 1.38 285 286putative protein 5E−25 At3g63070 1.35 287 288 hypothetical protein 0At4g28330 2.23 289 290 cellulose synthase catalytic subunit, putative1E−174 At1g55850 2.07 291 292 putative protein 0 At5g46410 1.54 293 294putative polynucleotide phosphorylase 1E−136 At3g03710 1.53 295 296hypothetical protein 0 At1g19180 1.32 297 298 hypothetical protein 0At3g12270 1.83 299 300 sugar transporter like protein 0 At4g36670 2.27301 302 hypothetical protein 1E−105 At2g39910 1.3 303 304 putativephytochrome A 0 At1g09570 2.45 305 306 hypothetical protein 0 At1g646001.49 307 308 putative protein 0 At5g23610 1.6 309 310 putative protein1E−177 At3g56360 1.39 311 312 cyclophylin - like protein 0 At3g634001.33 313 314 unknown protein 0 At2g37940 1.35 315 316 zinc fingerprotein, putative 1E−53 At1g75540 1.46 317 318 putative protein kinase1E+00 At2g24360 1.48 319 320 putative glucosyltransferase 0 At2g154902.15 321 322 unknown protein 0 At1g60140 1.72 323 324 unknown protein 0At1g43850 1.45 325 326 hypothetical protein 0 At3g14120 1.77 327 328putative AP2 domain transcription factor 0 At2g41710 1.65 329 330transcriptional regulator protein, putative 6E−71 At3g26640 1.51 331 332hypothetical protein 3E−02 At1g55370 1.35 333 334 unknown protein 0At3g28920 1.93 335 336 hypothetical protein 0 At3g03750 1.43 337 338hypothetical protein 2E+00 At4g27610 1.34 339 340 translation initiationfactor elF-2 beta chain - like protein 2E+00 At5g20920 1.33 341 342unknown protein 0 At2g26280 1.53 343 344 unknown protein 0 At1g784201.39 345 346 elongation factor, putative 3E+00 At1g56070 1.99 347 348anthranilate N-benzoyltransferase - like protein 1E−120 At5g01210 1.66349 350 putative protein 1E−178 At4g39680 1.43 351 352 unknown protein 0At3g05380 1.92 353 354 splicing factor At-SRp40 0 At4g25500 1.52 355 356cdc2-like protein kinase 0 At5g10270 1.77 357 358 calcium-dependentprotein kinase 1E−169 At3g57530 1.39 359 360 phosphoprotein phosphatase,type 1 catalytic subunit 0 At2g29400 1.48 361 362 putative mitochondrialtranslation elongation factor G 0 At2g45030 1.65 363 364long-chain-fatty-acid-CoA ligase-like protein 0 At5g27600 1.34 365 366cytochrome c, putative 4E−26 At3g27240 1.36 367 368 En/Spm-liketransposon protein 0 At2g40070 1.41 369 370 putative phospho-ser/thrphosphatase 0 At4g03080 1.41 371 372 chloroplast 50S ribosomal proteinL22, putative 6E−77 At1g52370 1.4 373 374 unknown protein 0 At2g158901.34 375 376 putative protein 0 At4g26750 1.55 377 378 receptor-proteinkinase-like protein 0 At5g54380 2.59 379 380 phosphoglycerate kinase,putative 1E−155 At3g12780 1.88 381 382 putative HMG protein 0 At2g175601.45 383 384 hypothetical protein 0 At1g76100 1.36 385 386 proteinkinase cdc2 homolog B 0 At3g54180 2.39 387 388 T-complex protein 1, betasubunit 0 At5g20890 1.39 389 390 proline oxidase, mitochondrialprecursor (osmotic stress-induced) 0 At3g30775 1.45 391 392 linkerhistone protein, putative 1E−126 At1g14900 1.33 393 394 hypotheticalprotein 0 At1g27500 2.21 395 396 ARF1-binding protein 0 At5g62010 1.58397 398 putative protein 0 At5g16270 1.37 399 400 putative protein1E−173 At5g13850 1.32 401 402 src-2 like protein 0 At1g09070 2.19 403404 RAN2 small Ras-like GTP-binding nuclear protein (Ran-2) 0 At5g200201.3 405 406 phosphoprotein phosphatase (PPX-1) 0 At4g26720 1.42 407 408nuclear protein-like 0 At5g64270 1.45 409 410 omithinecarbamoyltransferase precursor 0 At1g75330 1.41 411 412 unknown protein0 At2g41650 1.67 413 414 putative protein 0 At5g17640 1.66 415 416hypothetical protein 0 At1g57990 2.02 417 418 hypothetical protein 0At4g15760 1.64 419 420 glycine-rich protein 2 (GRP2) 0 At4g38680 1.72421 422 hypothetical protein 1E−113 At2g41780 2.6 423 424 RNA-bindingprotein, putative 8E−95 At3g20250 1.46 425 426 gda-1, putative 2E+00At3g27090 1.46 427 428 beta-fructofuranosidase 1 0 At3g13790 1.32 429430 26S proteasome subunit 4-like protein 0 At4g29040 1.51 431 432putative protein 1E−59 At1g33980 1.42 433 434 hypothetical protein 0At1g57680 2.66 435 436 unknown protein 0 At1g29980 1.98 437 438 60Sribosomal protein - like 0 At5g02870 1.39 439 440 REVOLUTA orinterfascicular fiberless 1 0 At5g60690 1.34 441 442 RAC-likeGTP-binding protein ARAC4 1E−180 At1g20090 1.78 443 444 unknown protein2E−42 At3g07390 1.34 445 446 unknown protein 0 At5g65660 1.7 447 448unknown protein 1E−154 At3g05040 1.52 449 450 putative DNA gyrasesubunit A 1E−153 At3g10690 2.2 451 452 putative protein 0 At3g49170 1.53453 454 eukaryotic cap-binding protein (gb|AAC17220.1) 0 At5g18110 1.41455 456 phosphoethanolamine N-methyltransferase, putative 0 At1g736001.62 457 458 unknown protein 0 At2g30590 2.78 459 460 RAN1 smallRas-like GTP-binding nuclear protein (Ran-1) 0 At5g20010 1.46 461 462putative protein 1E−104 At4g24290 1.32 463 464 putative auxin-regulatedprotein 0 At2g45210 1.33 465 466 adenylosuccinate synthetase 0 At3g576101.39 467 468 putative protein 0 At5g14530 2.7 469 470 putative ubiquitinactivating enzyme E1 (ECR1) 0 At5g19180 1.63 471 472 putativemitochondrial processing peptidase 0 At3g02090 1.4 473 474 putativeprotein 0 At3g48530 1.55 475 476 hypothetical protein 0 At1g20330 1.47477 478 hypothetical protein 0 At4g02590 1.36 479 480 putativepyrophosphate-fructose-6-phosphate 1- 0 At1g12000 1.49phosphotransferase 481 482 putative receptor-like protein kinase 0At2g02220 1.55 483 484 putative protein 1E−104 At4g02440 1.4 485 486non-phototropic hypocotyl, putative 0 At1g30440 1.57 487 488 histonedeacetylase 0 At5g63110 1.36 489 490 putative protein 0 At5g66580 3.18491 492 multicatalytic endopeptidase complex, proteasome precursor, 0At4g31300 1.42 beta 493 494 fibrillarin - like protein 6E−77 At4g256301.3 495 496 hypothetical protein 8E−45 At1g54060 1.36 497 498 histoneH1, partial 0 At2g30620 1.58 499 500 hypothetical protein 0 At3g090301.45 501 502 enoyl-CoA hydratase - like protein 0 At4g31810 1.31 503 504unknown protein 7E+00 At2g27080 1.51 505 506 myb-related transcriptionfactor, putative 0 At3g23250 1.49 507 508 Alcohol Dehydrogenase 0At1g77120 5.09 509 510 hypothetical protein 1E−132 At1g27590 1.38 511512 unknown protein 0 At1g14710 1.36 513 514 putative receptor-likeprotein kinase 0 At2g13790 1.68 515 516 putative protein 0 At5g145501.39 517 518 homeobox protein knotted-1 like 4 (KNAT4) 1E−165 At5g110601.4 519 520 putative protein 1E−142 At5g15540 1.47 521 522 carbonylreductase-like protein 7E+00 At5g51030 2.17 523 524 hypothetical protein1E−50 At1g53900 1.36 525 526 aspartate-tRNA ligase - like protein 0At4g31180 1.62 527 528 unknown protein 1E−121 At3g06150 1.74 529 530amino acid transporter protein-like 0 At5g65990 1.59 531 53212-oxophytodienoate reductase (OPR1) 0 At1g76680 1.43 533 534 calnexinhomolog 6E−25 At5g07340 1.39 535 536 unknown protein 0 At1g61100 2.06537 538 homogentisate 1,2-dioxygenase 1E−78 At5g54080 2.01 539 540glucosyltransferase - like protein 0 At4g34131 1.33 541 542 putativeprotein 4E−01 At5g54890 1.35 543 544 hypothetical protein 0 At1g760701.31 545 546 putative protein 1E−179 At5g18310 1.56 547 548 DNA bindingprotein ACBF - like 0 At5g19350 1.36 549 550 hypothetical protein 0At1g17210 1.69 551 552 putative protein 1E−111 At5g51220 1.46 553 554RING finger protein 0 At3g61460 2.14 555 556 putative protein 0At5g18580 1.32 557 558 putative protein kinase 0 At2g31010 1.35 559 560chloroplast nucleoid DNA binding protein, putative 0 At1g01300 1.49 561562 unknown protein 1E−143 At1g31130 1.4 563 564 splicing factor,putative 1E+00 At1g14650 1.56 565 566 putative TCP3 gb|AAC24010. 0At1g53230 1.38 567 568 unknown protein 0 At1g72790 1.71 569 570ribosomal protein S6 - like 0 At4g31700 1.38 571 572 auxin-resistanceprotein AXR1 0 At1g05180 1.36 573 574 putative protein 0 At5g11030 1.43575 576 putative 60S acidic ribosomal protein P0 0 At3g09200 1.47 577578 mismatch binding protein, putative 0 At3g24320 2.1 579 580 T-complexchaperonin protein, epsilon subunit 0 At1g24510 1.47 581 582 putativeprotein 0 At4g24120 1.56 583 584 putative protein 4E−38 At5g53900 1.79585 586 histidine transport protein (PTR2-B) 0 At2g02040 1.37 587 588unknown protein 0 At3g10490 1.43 589 590 tubulin alpha-5 chain-likeprotein 0 At5g19770 1.6 591 592 putative non-LTR retroelement reversetranscriptase 6E+00 At2g15510 4.71 593 594 unknown protein 1E−179At2g41010 1.33 595 596 putative chloroplast outer envelope 86-likeprotein 0 At4g02510 1.45 597 598 serine/threonine-specific proteinkinase NAK 0 At5g02290 1.56 599 600 unknown protein 0 At2g34680 1.45 601602 hypothetical protein 0 At1g43170 1.69 603 604 phospholipase D,putative, 5′ partial 0 At3g16785 1.5 605 606 CTP synthase-like protein 0At1g30820 1.58 607 608 nitrilase 2 0 At3g44300 1.84 609 610 putativemitogen activated protein kinase kinase 0 At3g04910 1.34 611 612putative protein 0 At4g27450 1.4 613 614 Phospholipase like protein 0At4g38550 1.9 615 616 endomembrane-associated protein 3E−41 At4g202601.83 617 618 leucine-rich receptor-like protein kinase, putative 0At1g72180 2.13 619 620 putative protein 8E−01 At4g25930 1.54 621 622WD-40 repeat protein MSI1 (sp|O22467) 0 At5g58230 1.72 623 624oxysterol-binding protein - like 1E−171 At5g59420 1.31 625 626 putativeprotein 1E−178 At4g21840 1.4 627 628 blue copper binding protein 1E−50At5g20230 2.3 629 630 UV-damaged DNA-binding protein - like 6E−9At4g21100 1.46 631 632 fatty acid hydroxylase (FAH1) 0 At2g34770 1.96633 634 putative thymidine kinase 0 At3g07800 8.44 635 636 hypotheticalprotein 0 At1g79380 1.41 637 638 unknown protein 0 At2g15860 1.36 639640 flower pigmentation protein ATAN11 0 At1g12910 1.41 641 642hypothetical protein 0 At1g56290 1.33 643 644 putative protein 0At3g62630 1.38 645 646 SNF-2 like RING finger 0 At1g61140 1.42 647 648unknown protein 0 At3g16310 1.49 649 650 putative glucosyl transferase 0At2g36800 1.36 651 652 putative protein 0 At4g25170 1.92 653 654hypothetical protein 9E−39 At4g00450 1.36 655 656 glutathioneS-transferase 0 At2g30860 1.49 657 658 unknown protein, 3′ partial 0At3g15095 1.42 659 660 unknown protein 0 At3g21080 1.31 661 662 TCH4protein (gb|AAA92363.1) 0 At5g57560 1.92 663 664 putative protein 0At3g61600 1.34 665 666 receptor-like kinase, putative 0 At3g23750 2.06667 668 putative 2,3-bisphosphoglycerate-independent phosphoglycerate 0At1g09780 1.34 669 670 putative protein 0 At5g14250 1.51 671 672 DnaJhomologue (gb|AAB91418.1|) 0 At5g06910 2.32 673 674 hypothetical protein0 At1g33250 1.35 675 676 unknown protein 0 At2g19800 1.81 677 678aspartate carbamoyltransferase precursor (aspartate 3E−84 At3g20330 1.49679 680 hypothetical protein 0 At1g16520 1.35 681 682 unknown protein5E+00 At1g48620 1.33 683 684 putative protein 1E+00 At4g35750 1.39 685686 hypothetical protein 1E−55 At3g13620 1.79 687 688 RNA helicase, DRH11E−179 At3g01540 1.56 689 690 putative 3-oxoacyl [acyl-carrier protein]reductase 0 At1g24360 1.42 691 692 putative cellular apoptosissusceptibility protein 1E−142 At2g46520 1.43 693 694 hypotheticalprotein 0 At1g01540 1.31 695 696 starch branching enzyme II 2E−61At2g36390 1.36 697 698 40S ribosomal protein - like 0 At5g15200 1.32 699700 putative protein 0 At4g13640 1.33 701 702 putative protein 0At3g45970 3.22 703 704 hypothetical protein 0 At1g66160 1.31 705 706 AP2domain containing protein RAP2.3 2E−9 At3g16770 1.51 707 708 putativeprotein 1E−47 At5g02880 1.32 709 710 NADH-dependent glutamate synthase 0At5g53460 2.25 711 712 arginine/serine rich splicing factor RSP3 4E−59At3g61860 1.31 713 714 hypothetical protein 1E−134 At1g55880 1.37 715716 translation initiation factor elF3 - like protein 6E−77 At4g209801.45 717 718 putative serine/threonine protein phosphatase catalyticsubunit, 0 At2g42500 1.38 719 720 unknown protein 1E−105 At1g33480 1.91721 722 COP1-interacting protein CIP8 0 At5g64920 1.4 723 724nonphototropic hypocotyl 1 6E+00 At3g45780 1.47 725 726 putative protein1E−78 At5g10860 1.32 727 728 putative protein 0 At5g19750 1.37 729 730putative protein 1E−127 At3g52500 1.39 731 732 putative protein 0At4g10280 1.76 733 734 cytochrome P450 monooxygenase 0 At4g31500 1.35735 736 ethylene responsive element binding factor 1E−104 At4g17500 1.33737 738 hypothetical protein 0 At1g17620 1.37 739 740 unknown protein1E−123 At3g07390 1.42 741 742 putative protein kinase 0 At3g02880 1.46743 744 DNA repair protein RAD23 homolog 0 At5g38470 1.42 745 746GTP-binding protein - like 1E−25 At5g03520 1.57 747 748 putative protein0 At3g63500 1.4 749 750 putative adenylate kinase 4E+00 At2g39270 1.37751 752 protein kinase - like 6E−46 At5g59010 1.42 753 754 unknownprotein 0 At3g04630 1.58 755 756 RNA binding protein 0 At1g73490 1.32757 758 putative phospholipase D 0 At3g15730 1.51 759 760 importin alpha1E−115 At3g06720 1.45 761 762 RING-H2 finger protein RHF2a 0 At5g220001.43 763 764 putative protein 2E−93 At4g19160 1.3 765 766 putativeprotein 0 At4g32440 1.41 767 768 putative protein phosphatase type 2C 0At3g15260 1.61 769 770 putative protein 0 At5g39890 1.31 771 772ribosomal protein 0 At4g16720 1.42 773 774 dormancy-associated protein9E+00 At1g28330 2.01 775 776 auxin-inducible gene (IAA2) 0 At3g230301.65 777 778 unknown protein 5E+00 At1g76010 1.54 779 780 protein kinaseADK1-like protein 1E+00 At4g28540 1.96 781 782 putative protein 0At4g24210 1.36 783 784 hypothetical protein 0 At1g79530 1.4 785 786putative trehalose-6-phosphate synthase 0 At1g68020 1.45 787 788adenylate kinase 0 At5g63400 1.39 789 790 putative proline-rich proteinprecursor 0 At1g73840 1.56 791 792 putative protein 5E−87 At5g14370 1.37793 794 hypothetical protein 0 At4g33290 1.7 795 796 cytochrome P450monooxygenase (CYP71B3) 0 At3g26220 1.32 797 798 TMV resistance proteinN - like 0 At4g19530 1.5 799 800 hypothetical protein 9E−70 At1g548301.33 801 802 3-ketoacyl-CoA thiolase 0 At2g33150 1.87 803 804 putativeprotein 0 At3g54350 1.35 805 806 hypothetical protein 1E−170 At4g026801.36 807 808 putative bHLH transcription factor 0 At2g46510 1.35 809 810RNA-binding protein, putative 5E−84 At3g26420 1.55 811 812 putativelectin 3E−20 At3g09190 1.67 813 814 xyloglucan endotransglycosylase,putative 0 At3g23730 2.85 815 816 unknown protein 2E−33 At2g41170 1.32817 818 putative protein 3E−78 At3g57150 1.67 819 820 putative glucoseregulated repressor protein 0 At2g25490 1.81 821 822 putative AP2 domaincontaining protein RAP2.4 gi|2281633 1E−150 At1g78080 1.82 823 824putative sulfate transporter 0 At1g80310 1.51 825 826 G protein alphasubunit 1 (GPA1) 0 At2g26300 1.44 827 828 protochlorophyllide reductaseprecursor 0 At4g27440 2.39 829 830 Shaggy related protein kinase tetha 0At4g00720 1.52 831 832 putative protein kinase 0 At3g01300 1.49 833 834RNA-binding protein-like protein 0 At3g47160 1.31 835 836 unknownprotein 1E−150 At5g24670 1.47 837 838 zinc finger protein ZFP8 1E−144At2g41940 1.42 839 840 GTP binding protein beta subunit 0 At4g34460 1.54841 842 copia-like retroelement pol polyprotein 0 At2g22680 1.4 843 844CONSTANS-like B-box zinc finger protein-like 0 At5g57660 1.36 845 846unknown protein 3E−71 At3g10640 1.33 847 848 putative protein 0At4g24690 1.91 849 850 NADH dehydrogenase 1E−124 At5g08530 1.42 851 852unknown protein 0 At1g73820 1.35 853 854 monosaccharide transportprotein, STP4 8E−9 At3g19930 1.58 855 856 globulin-like protein 0At1g07750 1.61 857 858 putative transitional endoplasmic reticulumATPase 2E−58 At3g09840 1.51 859 860 putative monodehydroascorbatereductase 0 At1g63940 1.39 861 862 anthranilatephosphoribosyltransferase like protein 0 At3g57880 1.42 863 864H+-transporting ATP synthase chain 9 - like protein 6E−25 At4g32260 1.83865 866 hypothetical protein 0 At1g02810 2.31 867 868 calmodulin-likeprotein 3E−63 At2g41410 1.52 869 870 putative protein 0 At5g15350 2.75871 872 glutathione S-transferase 0 At2g30870 1.54 873 874 putativeSWI/SNF complex subunit SW13 1E−138 At2g33610 1.32 875 876 MAP kinasekinase 2 0 At4g29810 1.39 877 878 adenosylhomocysteinase 1E−134At4g13940 2.07 879 880 putative protein 0 At5g27760 1.4 881 882 unknownprotein 0 At2g47450 1.67 883 884 putative protein 0 At4g33050 2.2 885886 50S ribosomal protein L12-C 1E−138 At3g27850 1.38 887 888 26Sproteasome AAA-ATPase subunit RPT4a (gb|AAF22524.1) 0 At5g43010 1.4 889890 unknown protein 8E−01 At3g01690 1.31 891 892 lipid transfer protein;glossy1 homolog 0 At5g57800 1.39 893 894 indoleacetic acid(IAA)-inducible gene (IAA7) 1E−7 At3g23050 1.52 895 896 histone H2B -like protein 0 At5g59910 2.16 897 898 putative RNA helicase 0 At3g064801.47 899 900 unknown protein 8E−64 At1g19310 1.44 901 902 unknownprotein 4E−96 At2g18440 1.38 903 904 unknown protein 0 At1g68220 1.59905 906 unknown protein 1E−142 At2g20570 1.35 907 908 putativereplication factor 1E−124 At1g21690 3.3 909 910 U2 snRNP auxiliaryfactor, small subunit 0 At5g42820 1.55 911 912 replication factor C -like 0 At5g27740 1.45 913 914 nuclear receptor binding factor-likeprotein 0 At3g45770 1.62 915 916 putative glycosyl transferase 0At1g24170 2.39 917 918 histone H2A-like protein 4E−53 At5g27670 1.62 919920 putative protein 1E−125 At5g48960 1.43 921 922 hypothetical protein0 At1g53740 1.42 923 924 splicing factor - like protein 0 At3g53500 1.39925 926 unknown protein 0 At1g50510 1.32 927 928 Fe(II) transportprotein 0 At4g19690 1.37 929 930 hypothetical protein 0 At1g61730 1.43931 932 unknown protein 7E−9 At2g47440 2.5 933 934 cold-regulatedprotein COR6.6 (KIN2) 0 At5g15970 3.03 935 936 putative cytochrome C 0At1g22840 1.3 937 938 unknown protein 0 At1g68580 2.13 939 940 putativeSer/Thr protein kinase 0 At1g16270 1.37 941 942 pseudogene 1E−138At2g25970 2.15 943 944 unknown protein 0 At3g06380 1.67 945 946 Tic22,putative 3E−84 At3g23710 2.14 947 948 unknown protein 0 At1g09250 1.55949 950 hypothetical protein 0 At1g72930 1.91 951 952 hypotheticalprotein 2E+00 At1g68820 1.43 953 954 histone H1 0 At2g18050 1.75 955 956unknown protein 0 At1g08630 1.45 957 958 unknown protein, 5′partial 0At3g18035 3.31 959 960 unknown protein 0 At1g04140 1.37 961 962 HAL3Aprotein 0 At3g18030 1.43 963 964 phi-1-like protein 0 At5g64260 3.38 965966 hypothetical protein 0 At1g12770 1.35 967 968 pollen specificprotein SF21 0 At5g56750 1.45 969 970 cysteine proteinase inhibitor likeprotein 1E−159 At4g16500 1.33 971 972 20S proteasome subunit C8(PAG1/PRC8 ARATH) 1E−130 At2g27020 1.36 973 974 nodulin-like protein1E−99 At1g75500 1.34 975 976 hypothetical protein 0 At1g72900 2.04 977978 hypothetical protein 0 At2g35230 1.42 979 980 arm repeat containingprotein homolog 0 At3g46510 1.4 981 982 putative protein 0 At5g674801.76 983 984 putative leucyl-tRNA synthetase 1E−118 At1g09620 1.52 985986 Putative UDP-glucose glucosyltransferase 1E−164 At1g22400 2.34 987988 alanine aminotransferase, putative 0 At1g17290 1.66 989 990 26Sproteasome AAA-ATPase subunit RPT6a 0 At5g19990 1.36 991 992 RuvDNA-helicase-like protein 0 At5g22330 1.59 993 994 small nuclearribonucleoprotein, putative 0 At1g65700 1.33 995 996 unknown protein 0At2g38310 2.79 997 998 protein phosphatase type 1 PP1BG 3E−91 At4g112401.51 999 1000 hypothetical protein 3E−41 At2g43410 2.1 1001 1002putative protein 0 At5g58600 1.42 1003 1004 nodulin-like protein 0At1g80530 2.07 1005 1006 putative protein 0 At5g56170 1.65 1007 1008dihydroxyacetone kinase, putative 1E−167 At3g17770 1.67 1009 1010ribsomal protein - like 1E−155 At5g09770 1.44 1011 1012 101 kDa heatshock protein; HSP101-like protein 0 At5g57710 1.34 1013 1014 unknownprotein 0 At5g51340 1.48 1015 1016 unknown protein 0 At3g05730 1.46 10171018 putative protein 2E+00 At5g67570 2.6 1019 1020 mitochondrialchaperonin (HSP60) 0 At2g33210 1.75 1021 1022 putative protein 1E−177At3g63270 1.34 1023 1024 growth factor like protein 0 At4g12720 1.781025 1026 RNA helicase, putative 0 At3g19760 1.54 1027 1028 pseudogene1E−142 At2g34760 1.81 1029 1030 hypothetical protein 0 At3g21740 1.521031 1032 shaggy-like kinase beta 0 At3g61160 1.36 1033 1034 unknownprotein 1E−165 At1g20100 1.35 1035 1036 24-sterol C-methyltransferase1E−143 At5g13710 1.41 1037 1038 WD-40 repeat protein (MSI3) 0 At4g350504.89 1039 1040 hypothetical protein 0 At1g67120 1.51 1041 1042 putativeprotein (fragment) 0 At5g14930 1.46 1043 1044 putative protein 1E−6At5g54180 1.78 1045 1046 hypothetical protein 1E−126 At1g20570 1.43 10471048 calcium-dependent protein kinase 0 At5g66210 2.96 1049 1050nitrilase 2 1E−127 At3g44300 1.88 1051 1052 methionyl-tRNA synthetase -like protein 1E−173 At4g13780 1.33 1053 1054 putative protein 0At4g24230 1.58 1055 1056 putative protein 2E−76 At5g19330 1.33 1057 1058caffeoyl-CoA O-methyltransferase - like protein 1E−166 At4g34050 1.411059 1060 putative DNA binding protein 0 At4g27000 1.43 1061 1062unknown protein 0 At1g55270 1.4 1063 1064 carbamoyl phosphate synthetaselarge chain (carB) 0 At1g29900 1.5 1065 1066 hypothetical protein 6E+00At4g02680 2.73 1067 1068 putative RNA helicase 0 At3g22310 1.53 10691070 molybdopterin synthase sulphurylase (gb|AAD18050.1) 0 At5g551301.77 1071 1072 inner mitochondrial membrane protein, putative 0At1g17530 1.55 1073 1074 putative protein kinase 0 At3g08760 1.9 10751076 putative JUN kinase activator protein 0 At1g22920 1.42 1077 1078thaumatin, putative 0 At1g75800 1.56 1079 1080 DNA-binding protein 0At3g14230 1.54 1081 1082 unknown protein 0 At2g01710 1.34 1083 1084putative calcium binding protein 0 At2g43290 1.57 1085 1086 class 1non-symbiotic hemoglobin (AHB1) 5E−93 At2g16060 1.86 1087 1088glycine-rich RNA binding protein, putative 2E−52 At3g23830 1.38 10891090 unknown protein 2E−37 At2g01190 1.3 1091 1092 hydoxyethylthiazolekinase, putative 2E−71 At3g24030 1.35 1093 1094 putative proteintranslocase 0E+00 At2g37410 1.51 1095 1096 putative protein 5E−02At5g61560 1.31 1097 1098 hypothetical protein 7E−02 At1g35600 1.56 10991100 ethylene-insensitive 3 0 At3g20770 1.5 1101 1102 lipoxygenaseAtLOX2 0 At3g45140 1.57 1103 1104 putative phosphatidic acid phosphatase0 At2g01180 1.85 1105 1106 unknown protein 5E−5 At1g80860 1.3 1107 1108unknown protein 2E−15 At3g28180 1.64 1109 1110 LOB domain protien 41 0At3g02550 4.01 1111 1112 putative protein 2E−02 At5g22260 1.95 1113 1114actin - like protein 1E−180 At3g60830 1.36 1115 1116 DEAD-box proteinabstrakt 0 At5g51280 1.53 1117 1118 putative DNA polymerase epsiloncatalytic subunit 2E+00 At2g27120 2.87 1119 1120 unknown protein 6E−59At5g48020 1.4 1121 1122 protein kinase C inhibitor-like protein 0At3g56490 1.58 1123 1124 putative PRP19-like spliceosomal protein 0At2g33340 1.7 1125 1126 germin-like protein 0 At1g72610 1.67 1127 1128putative protein 1E−5 At5g10050 1.32 1129 1130 putative protein 0At4g34950 1.96 1131 1132 zinc finger protein 0 At5g66730 1.37 1133 1134chaperonin gamma chain - like protein 1E−176 At5g26360 1.67 1135 1136WD-40 protein 7E+00 At4g07410 1.42 1137 1138 putative DNA-bindingprotein 0 At4g12080 1.4 1139 1140 beta-glucosidase, putative 0 At1g524001.66 1141 1142 hypothetical protein 1E−44 At2g23140 1.66 1143 1144homeobox protein 1E−43 At3g61150 1.63 1145 1146 glycine-rich protein 0At4g36020 1.82 1147 1148 unknown protein 0 At3g01460 1.37 1149 1150hypothetical protein 1E−134 At4g28190 1.4 1151 1152 predicted protein5E−37 At4g32010 1.34 1153 1154 N-myristoyl transferase 1E−157 At5g570201.37 1155 1156 putative protein 0 At4g36780 1.61 1157 1158 unknownprotein 2E−01 At5g48240 1.64 1159 1160 unknown protein 0 At1g21630 1.551161 1162 unknown protein 1E−102 At1g07360 1.74 1163 1164 lysyl-tRNAsynthetase 1E−96 At3g11710 1.38 1165 1166 unknown protein 0 At3g077801.51 1167 1168 tryptophan synthase beta chain 1 precursor (sp|P14671)1E−102 At5g54810 1.55 1169 1170 putative protein 8E−98 At4g25620 1.811171 1172 RuvB DNA helicase-like protein 0 At5g67630 1.32 1173 1174putative pectin methylesterase 0 At3g14310 1.43 1175 1176 putativecytidine deaminase 0 At2g19570 1.41 1177 1178 hypothetical protein 0At3g12400 1.42 1179 1180 1-aminocyclopropane-1-carboxylate synthase -like protein 0 At4g26200 1.54 1181 1182 peroxidase 3E−88 At2g38380 2.111183 1184 2-oxoglutarate dehydrogenase, E1 component 0 At5g65750 1.441185 1186 xylosidase 0 At5g49360 1.93 1187 1188 ethylene responsiveelement binding factor 4 0 At3g15210 1.7 1189 1190 putative protein2E+00 At5g46650 3.54 1191 1192 eukaryotic protein synthesis initiationfactor 4A 0 At3g13920 1.35 1193 1194 Unknown protein 0 At1g76970 2.341195 1196 hypothetical protein 0 At1g19380 1.54 1197 1198 unknownprotein 0 At5g49640 1.78 1199 1200 putative xyloglucan-specificglucanase 0 At2g01850 1.58 1201 1202 similar to nucellin gb|AAB96882.11E−106 At1g49050 1.5 1203 1204 unknown protein 0 At3g29390 1.33 12051206 putative protein 0 At3g62190 1.58 1207 1208 putative malatedehydrogenase 0 At1g04410 1.34 1209 1210 putative isocitrate lyase1E−153 At3g21720 3.08 1211 1212 DNA-binding protein 1E−160 At3g142301.48 1213 1214 histone H4-like protein 0 At3g46320 2.55 1215 1216putative dehydrogenase 0 At1g71170 1.47 1217 1218 alanine - tRNA ligase,putative 0 At1g50200 1.38 1219 1220 oligopeptidase A - like protein1E−172 At5g10540 1.43 1221 1222 putative protein 0 At5g62620 1.32 12231224 permease 0 At5g49990 1.3 1225 1226 DEAD BOX RNA helicase RH151E−129 At5g11200 1.4 1227 1228 lipoamide dehydrogenase precursor 1E−128At3g17240 1.38 1229 1230 hypothetical protein 0 At1g15170 1.75 1231 1232xyloglucan endo-1,4-beta-D-glucanase (XTR-6) 0 At4g25810 1.95 1233 1234histone H2B like protein (emb|CAA69025.1) 7E−34 At5g22880 1.91 1235 1236S-receptor kinase homolog 2 precursor 1E+00 At5g60900 2.61 1237 1238 60Sribosomal protein L2 7E−48 At2g18020 1.58 1239 1240 unknown protein 0At1g23030 1.98 1241 1242 zinc finger protein, putative 0 At1g34370 1.511243 1244 putative protein 3E−8 At4g05150 1.38 1245 1246 aldose1-epimerase - like protein 5E−25 At3g47800 1.88 1247 1248 cinnamoyl-CoAreductase - like protein 0 At5g58490 1.35 1249 1250 putativeNADP-dependent glyceraldehyde-3-phosphate 0 At2g24270 1.43 dehydrogenase1251 1252 isp4 like protein 0 At4g16370 1.77 1253 1254 putative protein0 At4g08350 1.32 1255 1256 calmodulin-related protein 2, touch-induced(TCH2) 0 At5g37770 1.55 1257 1258 20S proteasome subunit PAD2(gb|AAC32059.1) 0 At5g66140 1.5 1259 1260 glucosidase II alpha subunit 0At5g63840 1.35 1261 1262 putative GAR1 protein 0 At3g03920 1.74 12631264 putative protein 3E−45 At5g08450 1.79 1265 1266 glutamatedehydrogenase (EC 1.4.1.—) 1 (pir||S71217) 0 At5g18170 1.47 1267 1268putative protein 0 At5g06660 1.32 1269 1270 Nonclathrin coat proteingamma - like protein 1E−143 At4g34450 1.43 1271 1272 unknown protein 0At3g17860 1.6 1273 1274 similar to senescence-associated protein 0At2g23810 1.59 1275 1276 putative protein 0 At5g60420 1.31 1277 1278unknown protein 0 At1g28260 1.36 1279 1280 shaggy-like protein kinaseetha (EC 2.7.1.—) 0 At4g18710 1.37 1281 1282 putative 26S proteaseregulatory subunit 6A 0 At1g09100 1.47 1283 1284 unknown protein 0At3g21140 1.49 1285 1286 dynamin-like protein 0 At2g14120 1.4 1287 1288scarecrow-like 1 2E−47 At1g21450 1.75 1289 1290 unknown protein 7E−40At3g02710 1.3 1291 1292 putative protein 0 At5g50670 1.41 1293 1294helicase-like protein 1E−108 At5g44800 1.5 1295 1296 dynamin-likeprotein 4 (ADL4) 1E−100 At3g60190 1.32 1297 1298 unknown protein 0At3g12790 1.31 1299 1300 putative Tub family protein 0 At2g47900 1.371301 1302 putative protein 1E−119 At5g13020 1.33 1303 1304 alanineaminotransferase, putative 1E−147 At1g17290 1.36 1305 1306SCARECROW-like protein 0 At4g36710 1.49 1307 1308 alphagalactosyltransferase-like protein 0 At3g62720 3.26 1309 1310 putativeprotein 0 At4g31980 1.32 1311 1312 putative protein 1E−124 At3g564801.34 1313 1314 histone acetyltransferase HAT B 0 At5g56740 2.36 13151316 putative phosphoribosyl pyrophosphate synthetase 3E−97 At2g445301.45 1317 1318 AIG1 1E−130 At1g33960 1.45 1319 1320 hypothetical protein0 At4g22190 1.69 1321 1322 hypothetical protein 0 At1g26180 1.33 13231324 putative protein 4E−84 At5g59000 1.61 1325 1326 hypotheticalprotein 0 At2g27660 1.66 1327 1328 unknown protein 0 At1g33400 1.38 13291330 helicase-like protein 0 At5g44800 1.63 1331 1332 putative protein 0At5g44920 1.43 1333 1334 putative RNA-binding protein 0 At1g22910 2.131335 1336 meiosis specific - like protein 0 At5g02820 2.62 1337 1338isocitrate dehydrogenase - like protein 0 At5g14590 1.43 1339 1340hypothetical protein 1E−139 At1g15500 1.63 1341 1342 putative protein3E−01 At5g52270 1.38 1343 1344 ABC transporter-like protein 0 At5g065301.63 1345 1346 heat-shock protein 90, putative 0 At1g27640 1.48 13471348 unknown protein 0 At3g07220 1.33 2713 2714 large subunit ofribulose-1,5-bisphosphate NP_051067 4.71 carboxylase/oxygenase 2715 2716ribosomal protein L33 NP_051080 3.54 2717 2718 PSII I protein NP_0510742.81 2719 2720 ribosomal protein L2 NP_051099 2.61 2721 2722ATP-dependent protease subunit NP_051083 2.60 2723 2724 cytochrome B6NP_051088 2.55 2725 2726 ATPase epsilon subunit NP_051065 2.17 2728 272926S ribosomal RNA protein NP_085475 2.87 2729 2730 GATA Zn-fingerprotein At3g16870 2.75 2731 2732 unknown protein At5g53740 2.01 27332734 putative glucosyltransferase At2g15480 2.15 2735 2736Anthocyaninless2 At4g00730 2.73 2737 2738 pectate lyase-like proteinAt3g54920 2.13 2739 2740 putative sterol dehydrogenase At2g43420 2.10***This accession number was replaced by a new annotation and calledAt1g36160

TABLE 5 Arabidopsis genes 1.3 times (1/ratio) or more repressed inE2Fa/Dpa plants SEQ ID NO cDNA PROT Gene name E-value MIPS accessionNumber Ratio 1349 1350 putative glutathione peroxidase 0 At2g31570 0.511351 1352 phenylalanine ammonia lyase (PAL1) 0 At2g37040 0.65 1353 1354unknown protein 0 At1g04040 0.62 1355 1356 putative protein 0 At4g253400.52 1357 1358 water channel - like protein 1E−129 At4g23400 0.7 13591360 catalase 0 At4g35090 0.46 1361 1362 stearoyl-ACP desaturase 2E−11At2g43710 0.54 1363 1364 putative oligopeptide transporter 0 At4g107700.37 1365 1366 putative chloroplast 50S ribosomal protein L28 0At2g33450 0.73 1367 1368 ferredoxin - NADP reductase precursor, putative0 At1g20020 0.64 1369 1370 3-beta-hydroxysteroid dehydrogenase 1E−44At2g26260 0.73 1371 1372 putative alanine aminotransferase 1E−127At1g70580 0.51 1373 1374 hypothetical protein 4E−99 At1g56500 0.66 13751376 putative protein 0 At5g21940 0.64 1377 1378 putative protein 1E−158At5g26970 0.7 1379 1380 actin depolymerizing factor 4 - like protein 0At5g59890 0.66 1381 1382 hypothetical protein 7E−72 At3g45160 0.5 13831384 transporter-like protein 1E−07 At3g53960 0.68 1385 1386nicotianamine synthase (dbj|BAA74589.1) 0 At5g04950 0.35 1387 1388cytochrome P450 monooxygenase (CYP83A1) 0 At4g13770 0.39 1389 1390unknown protein 0 At2g29660 0.77 1391 1392 hypothetical protein 0At3g12580 0.56 1393 1394 unknown protein 0 At5g64130 0.52 1395 1396putative protein 0 At3g61870 0.73 1397 1398 fructose-bisphosphatealdolase - like protein 0 At4g26530 0.17 1399 1400 lectin like protein1E−124 At4g19840 0.74 1401 1402 unknown protein 0 At1g28140 0.72 14031404 feebly-like protein 0 At3g01420 0.73 1405 1406 beta-fructosidase1E−105 At1g62660 0.38 1407 1408 unknown protein 1E−06 At1g15350 0.771409 1410 peptidylprolyl isomerase ROC1 0 At4g38740 0.76 1411 1412hypothetical protein 1E−36 At2g06010 0.74 1413 1414 putative protein1E−114 At4g30490 0.5 1415 1416 3-isopropylmalate dehydrogenase 0At5g14200 0.61 1417 1418 putative copper/zinc superoxide dismutase 1E−93At2g28190 0.77 1419 1420 putative myo-inositol 1-phosphate synthase 0At2g22240 0.68 1421 1422 putative enolase (2-phospho-D-glyceratehydroylase) 0 At2g29560 0.7 1423 1424 unknown protein 0 At5g43750 0.41425 1426 putative protein 1E−22 At4g32330 0.68 1427 1428 putativeferredoxin-thioredoxin reductase 0 At2g04700 0.75 1429 1430 hypotheticalprotein 1E+00 At3g23290 0.59 1431 1432 putative cellulose synthase 0At2g32530 0.58 1433 1434 putative protein 0 At5g43650 0.54 1435 1436putative protein 0 At5g03010 0.58 1437 1438 hypothetical protein 0At1g78140 0.61 1439 1440 unknown protein 0 At1g72590 0.35 1441 1442hypothetical protein 0 At1g54450 0.59 1443 1444 hypothetical protein 0At1g19110 0.73 1445 1446 endo-beta-1,4-glucanase, putative 0 At1g756800.7 1447 1448 unknown protein 0 At1g63010 0.76 1449 1450 hypotheticalprotein 2E−58 At4g24700 0.57 1451 1452 glyoxalase II 0 At1g53580 0.651453 1454 putative protein 0 At3g52370 0.53 1455 1456 unknown protein 0At1g80280 0.57 1457 1458 protein phosphatase ABI1 0 At4g26080 0.71 14591460 33 kDa polypeptide of oxygen-evolving complex (OEC) in 1E−115At5g66570 0.65 photosystem 1461 1462 beta-xylosidase 1E−163 At5g645700.55 1463 1464 GDP-mannose pyrophosphorylase 0 At2g39770 0.62 1465 1466peroxidase ATP20a (emb|CAA67338.1) 0 At5g14130 0.67 1467 1468 putativeglutathione transferase 0 At1g17190 0.71 1469 1470 putative protein 0At4g38080 0.75 1471 1472 unknown protein 1E−179 At1g61190 0.7 1473 147450S ribosomal protein L24, chloroplast precursor 0 At5g54600 0.76 14751476 unknown protein 1E−179 At1g68260 0.55 1477 1478 subtilisin-likeserine proteinase, putative, 3′ partial 0 At3g14067 0.62 1479 1480putative protein 0 At4g23890 0.59 1481 1482 unknown protein 0 At3g016900.7 1483 1484 putative protein 0 At3g56290 0.3 1485 1486 unknown protein0 At2g39450 0.67 1487 1488 unknown protein 0 At5g64130 0.66 1489 1490putative protein 0 At4g30140 0.54 1491 1492 ribulose bisphosphatecarboxylase small chain 3b precursor 1E−145 At5g38410 0.54 (RuBisCO 14931494 Myb DNA binding protein - like 0 At3g46130 0.75 1495 1496 putative2-cys peroxiredoxin 0 At3g11630 0.64 1497 1498 putative trypsininhibitor 0 At1g73260 0.59 1499 1500 O-methyltransferase 1E−127At5g54160 0.62 1501 1502 hypothetical protein 2E−30 At1g29270 0.73 15031504 RP19 gene for chloroplast ribosomal protein CL9 9E−67 At3g448900.68 1505 1506 putative phosphoglyceride transfer protein 1E−178At4g08690 0.57 1507 1508 putative protein 0 At5g63530 0.53 1509 1510putative protein 0 At5g38720 0.68 1511 1512 hypothetical protein 0At1g72030 0.68 1513 1514 unknown protein 9E−21 At5g09990 0.67 1515 1516zinc finger protein ZAT7 0 At3g46090 0.73 1517 1518 putative nodulin 0At3g05180 0.64 1619 1520 putative wound-induced basic protein 1E−160At3g07230 0.75 1521 1S22 hypothetical protein 0 At4g02920 0.38 1523 1524putative protein 1E−154 At5g62220 0.73 1525 1526 myosin heavy chain-likeprotein 0 At3g16000 0.5 1527 1528 unknown protein 0 At1g09610 0.76 15291530 arabinogalactan protein - like 0 At5g03170 0.71 1531 1532 biotincarboxyl carrier protein of acetyl-CoA carboxylase 0 At5g16390 0.69precursor 1533 1534 centrin 0 At3g50360 0.74 1535 1536 vegetativestorage protein Vsp1 0 At5g24780 0.48 1537 1538 protein kinase, putative1E−61 At1g52310 0.63 1539 1540 unknown protein 1E−132 At2g42760 0.631541 1542 phenylalanine ammonia lyase (PAL1) 0 At2g37040 0.72 1543 1544UDP rhamnose-anthocyanidin-3-glucoside rhamnosyltransferase - 0At4g27560 0.45 like 1545 1546 unknown protein 0 At2g17500 0.54 1547 1548NAC domain protein, putative 0 At1g01720 0.72 1549 1550ubiquitin-conjugating enzyme-like protein 2E−24 At5g56150 0.41 1551 1552putative RNA-binding protein 1E−136 At2g37220 0.72 1553 1554 Overlapwith bases 87, 142-90, 425 of ‘IGF’ BAC clone F9K20, 0 At1g78570 0.52accession 1555 1556 hypothetical protein 1E−105 At2g04040 0.52 1557 1558lsp4-like protein 4E−01 At5g64410 0.39 1559 1560 ids4-like protein 0At5g20150 0.58 1561 1562 unknown protein 3E−98 At1g44000 0.67 1563 1564R2R3-MYB transcription factor 0 At3g50060 0.66 1565 1566 putative hexosetransporter 0 At4g02050 0.68 1567 1568 one helix protein (OHP) 0At5g02120 0.57 1569 1570 UDP-glucose dehydrogenase-like protein 0At5g15490 0.74 1571 1572 putative protein 0 At3g54260 0.63 1573 1574putative L5 ribosomal protein 0 At4g01310 0.75 1575 1576 putative myosinheavy chain 0 At2g37080 0.61 1577 1578 clpB heat shock protein-like 0At5g15450 0.57 1579 1580 unknown protein 4E−71 At1g52510 0.66 1581 1582beta-fructosidase, putative 0 At1g12240 0.55 1583 1584 hypotheticalprotein 0 At1g47670 0.69 1585 1586 putative protein 3E−36 At5g25890 0.751587 1588 predicted protein 1E−108 At4g31390 0.73 1589 1590 putativephospholipase 0 At2g39420 0.66 1591 1592 ATP-dependent transmembranetransporter, putative 0 At1g51460 0.74 1593 1594 H+-transporting ATPsynthase-like protein 0 At4g09650 0.64 1595 1596 putative protein 0At4g29590 0.77 1597 1598 unknown protein 0 At3g02640 0.49 1599 1600phosphoenolpyruvate carboxylase (PPC) 0 At3g14940 0.77 1601 1602 pollenallergen-like protein 0 At1g24020 0.28 1603 1604 putative AUX1-likepermease 0 At1g77690 0.73 1605 1606 putative protein 1E−127 At4g397300.49 1607 1608 homeobox-leucine zipper protein ATHB-12 0 At3g61890 0.241609 1610 putative protein 0 At5g10160 0.53 1611 1612 unknown protein 0At1g71480 0.56 1613 1614 putative violaxanthin de-epoxidase precursor(U44133) 0 At1g08550 0.7 1615 1616 nClpP5, putative 0 At1g49970 0.681617 1618 hypothetical protein 0 At1g65260 0.57 1619 1620 putativeprotein 1E−135 At3g52360 0.38 1621 1622 putative protein 0 At5g26260 0.51623 1624 unknown protein 0 At1g25170 0.66 1625 1626 hypotheticalprotein 0 At1g79550 0.65 1627 1628 tubulin beta-2/beta-3 chain(sp|P29512) 2E−21 At5g62700 0.61 1629 1630 eukaryotic translationinitiation factor 4E, putative 0 At1g29550 0.64 1631 1632 transportinhibitor response 1, putative 1E−175 At1g12820 0.77 1633 1634 osmotinprecursor 1E−110 At4g11650 0.74 1635 1636 putative glutathioneS-transferase TSI-1 0 At1g10360 0.72 1637 1638 protein ch-42 precursor,chloroplast 0 At4g18480 0.76 1639 1640 omega-3 fatty acid desaturase2E−06 At2g29980 0.73 1641 1642 unknown protein 0 At2g44670 0.57 16431644 putative protein 0 At3g55330 0.51 1645 1646 putative calmodulin 0At3g51920 0.55 1647 1648 plastid ribosomal protein L34 precursor,putative 1E−140 At1g29070 0.69 1649 1650 putative protein 0 At5g670700.66 1651 1652 putative 2Fe-2S iron-sulfur cluster protein 0 At3g162500.69 1653 1654 hypothetical protein 0 At1g42970 0.69 1655 1656hypothetical protein 3E−69 At3g14190 0.6 1657 1658 thylakoid luminalprotein 1E−122 At1g77090 0.7 1659 1660 putative protein 0 At3g48420 0.421661 1662 actin 3 0 At2g37620 0.64 1663 1664 OEP8 like protein 4E−38At4g15800 0.73 1665 1666 putative Ras-like GTP-binding protein 0At3g09910 0.71 1667 1668 sulfolipid biosynthesis protein SQD1 0At4g33030 0.68 1669 1670 oleosin isoform 0 At3g27660 0.61 1671 1672acyl-CoA synthetase, putative 0 At1g64400 0.59 1673 1674 putativeprotein 1E−147 At3g61060 0.5 1675 1676 hypothetical protein 1E−117At1g56200 0.64 1677 1678 putative protein 0 At4g13500 0.53 1679 1680cinnamoyl CoA reductase, putative 0 At1g80820 0.72 1681 1682hypothetical protein 1E−157 At4g28410 0.1 1683 1684 hypothetical protein0 At1g54030 0.68 1685 1686 putative DNA-binding protein, GT-1 0At3g25990 0.1 1687 1688 germin-like protein 3E−04 At3g05950 0.49 16891690 putative glutathione S-transferase 0E+00 At2g29480 0.7 1691 1692arabinogalactan-protein (gb|AAC77823.1) 1E−06 At5g64310 0.61 1693 1694periaxin - like protein 1E−151 At5g09530 0.71 1695 1696 zeaxanthinepoxidase precursor 0 At5g67030 0.52 1697 1698 putative photosystem Ireaction center subunit IV 0 At2g20260 0.7 1699 1700 putative 60Sribosomal protein L18A 0 At3g14600 0.74 1701 1702 putative ethyleneresponse element binding protein (EREBP) 0 At2g44840 0.72 1703 1704unknown protein 0 At2g21970 0.5 1705 1706 RNA-binding protein cp33precursor 0 At3g52380 0.73 1707 1708 unknown protein 1E−152 At2g344600.62 1709 1710 CONSTANS-like 1 1E−179 At5g15850 0.6 1711 1712 unknownprotein 0 At1g75100 0.77 1713 1714 ion channel 9E−66 At1g15990 0.57 17151716 unknown protein 0 At2g21960 0.46 1717 1718 unknown protein 0At1g66330 0.69 1719 1720 putative protein 0 At4g26630 0.68 1721 1722unknown protein 1E−99 At3g28230 0.72 1723 1724 hypothetical protein1E−65 At1g55910 0.65 1725 1726 putative Na+-dependent inorganicphosphate cotransporter 0 At2g29650 0.52 1727 1728 hypothetical protein4E−23 At1g02330 0.71 1729 1730 hypothetical protein 0 At1g29700 0.551731 1732 putative flavonol 3-O-glucosyltransferase 0 At2g18560 0.621733 1734 lycopene epsilon cyclase 0 At5g57030 0.6 1735 1736hypothetical protein 0 At3g09150 0.75 1737 1738 putative protein 1E−150At1g31710 0.5 1739 1740 hypothetical protein 0 At1g78850 0.69 1741 1742putative protein 0 At4g32770 0.75 1743 1744 putative protein 2E−77At4g22890 0.75 1745 1746 ripening-related protein - like 0 At5g207400.59 1747 1748 putative peroxidase ATP12a 0 At1g05240 0.65 1749 1750hypothetical protein 7E−18 At4g01050 0.77 1751 1752 V-ATPase subunit G(vag2 gene) 4E−04 At4g23710 0.61 1753 1754 hypothetical protein 0At1g58080 0.75 1755 1756 putative protein 2E−94 At5g19190 0.51 1757 1758hypothetical protein 0 At1g48850 0.69 1759 1760 putative protein 0At4g38800 0.75 1761 1762 similar to polygalacturonase-like protein 0At1g10640 0.28 1763 1764 putative glutathione S-transferase 0 At2g023900.73 1765 1766 putative calcium-binding EF-hand protein 3E−78 At2g333800.69 1767 1768 unknown protein 1E−113 At1g64680 0.57 1769 1770 unknownprotein 0 At3g15660 0.58 1771 1772 putative protein 0 At5g22080 0.741773 1774 high mobility group protein 2-like 2E−24 At3g51880 0.71 17751776 similar to late embryogenesis abundant proteins 4E−50 At2g440600.61 1777 1778 putative protein 0 At4g34600 0.74 1779 1780 putativeprotein 2E−31 At5g52060 0.48 1781 1782 NADPH oxidoreductase, putative 0At1g75280 0.53 1783 1784 hypothetical protein 0 At1g16720 0.62 1785 1786unknown protein 0 At3g28130 0.75 1787 1788 glutaredoxin 0 At4g15690 0.731789 1790 putative protein 4E−01 At3g47590 0.66 1791 1792 putativeprotein 0 At4g26630 0.7 1793 1794 putative polyprotein 1E−139 At4g044100.76 1795 1796 MTN3-like protein 0 At3g48740 0.49 1797 1798 hypotheticalprotein 0 At1g32900 0.38 1799 1800 unknown protein 0 At2g33180 0.77 18011802 hypothetical protein 0 At1g66890 0.69 1803 1804 unknown protein 0At1g74730 0.74 1805 1806 putative ribosomal protein S9 1E−122 At1g749700.7 1807 1808 phenylalanine ammonia-lyase 3E−51 At3g53260 0.53 1809 1810unknown protein 2E−27 At1g78110 0.76 1811 1812 unknown protein 0At1g18300 0.75 1813 1814 putative prolylcarboxypeptidase 1E−174At2g24280 0.64 1815 1816 unknown protein 1E−12 At3g24100 0.76 1817 1818unknown protein 0 At3g18990 0.39 1819 1820 hypothetical protein 1E−127At1g78890 0.75 1821 1822 unknown protein 5E−87 At2g21530 0.71 1823 1824hypothetical protein 1E−172 At1g20340 0.71 1825 1826 putativeglucosyltransferase 0 At2g31790 0.63 1827 1828 allergen like protein1E−129 At4g17030 0.74 1829 1830 unknown protein 0 At1g73750 0.72 18311832 APG5 (autophagy 5)-like protein 0 At5g17290 0.7 1833 1834 putativeprotochlorophyllide reductase 0 At1g03630 0.57 1835 1836 zinc fingerprotein, putative 0 At3g19580 0.61 1837 1838 unknown protein 0 At2g351900.65 1839 1840 phosphate/triose-phosphate translocator precursor 4E−33At5g46110 0.73 (gb|AAC83815.1) 1841 1842 unknown protein 0 At5g508400.77 1843 1844 hypothetical protein 0 At4g34090 0.69 1845 1846hypothetical protein 0 At1g14340 0.64 1847 1848 unknown protein 0At1g67860 0.42 1849 1850 tyrosine transaminase like protein 1E−180At4g23600 0.47 1851 1852 unknown protein 1E−173 At1g53890 0.53 1853 1854pectinesterase, putative 0 At1g41830 0.76 1855 1856 putative protein4E−72 At5g45550 0.69 1857 1858 putative ligand-gated ion channel subunit2E+00 At2g32400 0.45 1859 1860 unknown protein 0 At3g19370 0.42 18611862 putative protein 5E−13 At5g62580 0.59 1863 1864 putative protein 0At3g61080 0.42 1865 1866 putative squamosa-promoter binding protein 21E−162 At1g27360 0.74 1867 1868 sucrose-phosphate synthase - likeprotein 0 At4g10120 0.22 1869 1870 hypothetical protein 4E−23 At1g621800.43 1871 1872 ribosomal protein 0 At4g15000 0.75 1873 1874 MYB-relatedtranscription factor (CCA1) 0 At2g46830 0.46 1875 1876pinoresinol-lariciresinol reductase, putative 1E−124 At1g32100 0.72 18771878 putative protein 0 At3g52230 0.71 1879 1880 3-keto-acyl-CoAthiolase 2 (gb|AAC17877.1) 0 At5g48880 0.57 1881 1882 putative protein 0At3g46780 0.63 1883 1884 DNA-binding protein, putative 0 At1g01060 0.621885 1886 putative protein 3E−20 At4g30990 0.6 1887 1888 putativeprotein 0 At3g46780 0.59 1889 1890 hypothetical protein 1E−174 At1g284000.58 1891 1892 DNA binding protein - like 0 At5g61600 0.55 1893 1894putative protein 0 At3g62260 0.72 1895 1896 putative CCCH-type zincfinger protein 0 At2g25900 0.63 1897 1898 ubiquitin-conjugating enzymeE2-17 kD 8 (ubiquitin-protein ligase 3E−16 At5g41700 0.42 1899 1900microbody NAD-dependent malate dehydrogenase 0 At5g09660 0.63 1901 1902glyceraldehyde 3-phosphate dehydrogenase A subunit (GapA) 0 At3g266500.63 1903 1904 microbody NAD-dependent malate dehydrogenase 0 At5g096600.66 1905 1906 sedoheptulose-bisphosphatase precursor 0 At3g55800 0.541907 1908 putative Fe(II) transporter 1E−175 At2g32270 0.74 1909 1910germin - like protein 0 At5g38940 0.75 1911 1912 putative malonyl-CoA:Acyl carrier protein transacylase 0 At2g30200 0.7 1913 1914 hypotheticalprotein 0 At1g19000 0.61 1915 1916 FRO1-like protein; NADPH oxidase-like0 At5g49740 0.41 1917 1918 J8-like protein 0 At1g80920 0.51 1919 1920putative protein 0 At4g34190 0.63 1921 1922 photosystem IIstability/assembly factor HCF136 (sp|O82660) 0 At5g23120 0.66 1923 1924hypothetical protein 0 At4g24930 0.63 1925 1926 2-cys peroxiredoxin-likeprotein 0 At5g06290 0.69 1927 1928 putative protein 0 At3g53470 0.541929 1930 unknown protein 3E−96 At3g02180 0.71 1931 1932 F12P19.7 0At1g65900 0.69 1933 1934 putative fibrillin 0 At4g04020 0.28 1935 1936putative protein 1E−01 At4g18810 0.72 1937 1938 hypothetical protein1E−171 At1g50240 0.67 1939 1940 putative protein 0 At3g63210 0.76 19411942 unknown protein 0 At2g32870 0.47 1943 1944 Glucose-1-phosphateadenylyltransferase (ApL1/adg2) 0 At5g19220 0.64 1945 1946 unknownprotein 1E−66 At2g46100 0.67 1947 1948 farnesyl diphosphate synthaseprecursor (gb|AAB49290.1) 0 At5g47770 0.71 1949 1950 pyridoxinebiosynthesis protein - like 0 At5g01410 0.47 1951 1952 hypotheticalprotein 0 At4g03820 0.71 1953 1954 putative myrosinase-binding protein1E−47 At2g39310 0.38 1955 1956 unknown protein 0 At1g05870 0.44 19571958 heat shock protein, putative 0 At1g06460 0.28 1959 1960 RIBOSOMALPROTEIN, putative 1E−175 At1g71720 0.76 1961 1962 elongation factor G,putative 0 At1g62750 0.65 1963 1964 mitochondrial Lon protease homolog 1precursor (sp|O64948) 0 At5g47040 0.76 1965 1966 cytochrome c 2E−37At4g10040 0.72 1967 1968 hypothetical protein 1E−102 At4g03420 0.69 19691970 putative DnaJ protein 1E−160 At2g41000 0.73 1971 1972 hypotheticalprotein 0 At2g27290 0.61 1973 1974 putative protein 1E−117 At5g50100 0.41975 1976 phytoene synthase (gb|AAB65697.1) 0 At5g17230 0.64 1977 1978putative protein 0 At4g28230 0.73 1979 1980 hypothetical protein 0At2g01260 0.49 1981 1982 unknown protein 0 At3g17520 0.71 1983 1984 Ranbinding protein (AtRanBP1b) 0 At2g30060 0.73 1985 1986 putative protein0 At4g32190 0.63 1987 1988 unknown protein 0 At1g19400 0.64 1989 1990sucrose-phosphate synthase-like protein 0 At5g20280 0.67 1991 1992putative protein 1E−136 At5g03545 0.45 1993 1994 biotin carboxyl carrierprotein precursor-like protein 1E−124 At5g15530 0.54 1995 1996 unknownprotein 4E−85 At1g16320 0.53 1997 1998 unknown protein 5E−16 At3g329300.68 1999 2000 putative protein 1E−142 At4g35290 0.74 2001 2002glutathione S-transferase-like protein 0 At5g17220 0.66 2003 2004fructose 1,6-bisphosphatase, putative 0 At1g43670 0.63 2005 2006peptidylprolyl isomerase-like protein 2E−34 At5g13120 0.72 2007 2008teosinte branched1 - like protein 0 At4g18390 0.63 2009 2010 putativeprotein 0 At3g51520 0.71 2011 2012 lactoylglutathione lyase-like protein0 At1g11840 0.45 2013 2014 late embryogenesis abundant protein LEA like0 At5g06760 0.55 2015 2016 putative protein 1E−177 At5g19590 0.71 20172018 putative protein 0 At3g63190 0.72 2019 2020 hypothetical protein 0At1g69510 0.47 2021 2022 putative protein kinase 0 At2g30040 0.69 20232024 xyloglucan endo-transglycosylase 0 At3g44990 0.43 2025 2026phospholipid hydroperoxide glutathione peroxidase 0 At4g11600 0.71 20272028 sedoheptulose-bisphosphatase precursor 0 At3g55800 0.51 2029 2030Clp proteinase like protein 2E−55 At4g17040 0.75 2031 2032 unknownprotein 0 At5g07020 0.68 2033 2034 unknown protein 2E−32 At5g51720 0.492035 2036 endomembrane protein, putative 1E−117 At1g14670 0.75 2037 2038putative phosphomannomutase 0 At2g45790 0.66 2039 2040 putative protein1E−95 At4g27280 0.46 2041 2042 mrp protein, putative 0 At3g24430 0.752043 2044 putative vacuolar ATPase 0 At4g02620 0.74 2045 2046 phosphatetransporter, putative 0 At3g26570 0.61 2047 2048 similar to Trp Asprepeat protein emb|CAB39845.1; similar to EST 0 At1g78070 0.74 2049 2050putative MAP kinase 2E−18 At2g01450 0.51 2051 2052 ethylene-responsivetranscriptional coactivator, putative 0 At3g24500 0.51 2053 20546-phosphogluconolactonase-like protein 0 At5g24420 0.52 2055 2056beta-amylase-like proten 1E−175 At5g18670 0.4 2057 2058 hypotheticalprotein 3E−53 At1g20970 0.72 2059 2060 chloroplast 50S ribosomal proteinL31, putative 0 At1g75350 0.74 2061 2062 cytochrome P450-like protein 0At4g37320 0.67 2063 2064 putative potassium transporter AtKT5p (AtKT5) 0At4g33530 0.76 2065 2666 putative ribosomal-protein S6 kinase (ATPK6) 0At3g08730 0.63 2067 2068 hypothetical protein 0 At1g04770 0.68 2069 2070transcription factor Hap5a 6E−74 At3g48590 0.6 2071 2072 putativeprotein 0 At5g20070 0.69 2073 2074 beta-expansin 0 At2g20750 0.72 20752076 SOUL-like protein 4E−82 At1g17100 0.71 2077 2078 unknown protein 0At1g70760 0.4 2079 2080 unknown protein 1E−124 At2g20890 0.73 2081 2082unknown protein 1E−160 At1g07280 0.72 2083 2084 unknown protein 0At1g64680 0.65 2085 2086 ADPG pyrophosphorylase small subunit(gb|AAC39441.1) 0 At5g48300 0.68 2087 2088 unknown protein 0 At2g173400.61 2089 2090 hypothetical protein 0 At1g26800 0.74 2091 2092 unknownprotein 0 At1g22930 0.67 2093 2094 polyphosphoinositide binding protein,putative 0 At1g01630 0.72 2095 2096 caffeoyl-CoA O-methyltransferase -like protein 0 At4g34050 0.67 2097 2098 pectinesterase 0 At5g53370 0.562099 2100 unknown protein 7E−75 At1g64370 0.43 2101 2102p-nitrophenylphosphatase-like protein 0 At5g36790 0.52 2103 2104putative protein 1E−172 At5g55960 0.64 2105 2106 serine/threonineprotein kinase - like protein 0 At5g10930 0.26 2107 2108 cytosolicfactor, putative 0 At1g72160 0.67 2109 2110 S-adenosylmethionine:2-demethylmenaquinone 1E−159 At5g56260 0.76 methyltransferase-like 21112112 pactate lyase 0 At5g63180 0.67 2113 2114 vacuolar sortingreceptor-like protein 0 At4g20110 0.7 2115 2116 putative membranechannel protein 0 At2g28900 0.76 2117 2118 putative thylakoid lumenrotamase 0 At3g01480 0.56 2119 2120 putative chloroplast prephenatedehydratase 0 At3g44720 0.73 2121 2122 3-oxoacyl-[acyl-carrier-protein]synthase I precursor 0 At5g46290 0.76 2123 2124 P-Protein - like protein1E−108 At4g33010 0.73 2125 2126 NHE1 Na+/H+ exchanger 1E−122 At5g271500.73 2127 2128 receptor kinase-like protein 0 At3g47580 0.72 2129 2130raffinose synthase - like protein 0 At5g40390 0.59 2131 2132 thylakoidluminal protein 0 At1g54780 0.63 2133 2134 unknown protein 0 At2g461700.73 2135 2136 beta-xylan endohydrolase - like protein 9E−02 At4g338100.26 2137 2138 putative protein 1E−137 At4g12700 0.6 2139 2140 putativeribose 5-phosphate isomerase 0 At3g04790 0.76 2141 2142 putative protein0 At5g47840 0.7 2143 2144 putative RNA-binding protein 0 At1g09340 0.572145 2146 adenine phosphoribosyltransferase (EC 2.4.2.7) - like protein0 At4g22570 0.46 2147 2148 unknown protein 0 At3g15950 0.37 2149 2150putative glutathione peroxidase 7E−12 At2g25080 0.46 2151 2152 putativeprotein 0 At5g23060 0.63 2153 2154 pectate lyase 1-like protein 0At1g67750 0.42 2155 2156 putative triosephosphate isomerase 9E−61At2g21170 0.66 2157 2158 carbonate dehydratase - like protein 0At4g33580 0.72 2159 2160 putative protein 0 At5g37300 0.56 2161 2162putative protein 1E−143 At3g60080 0.77 2163 2164 cystatin(emb|CAA03929.1) 2E−83 At5g12140 0.74 2165 2166 putative cytochrome b5 0At2g46650 0.46 2167 2168 putaive DNA-binding protein 2E−08 At4g315500.63 2169 2170 hypothetical protein 1E−143 At3g21050 0.5 2171 2172putative beta-hydroxyacyl-ACP dehydratase 0 At2g22230 0.59 2173 21742-oxoglutarate/malate translocator 0 At5g64290 0.77 2175 2176hypothetical protein 1E−123 At3g27050 0.49 2177 2178 putative alcoholdehydrogenase 9E−64 At2g37770 0.64 2179 2180 hypothetical protein 1E−107At1g18730 0.67 2181 2182 putative pectinacetylesterase 0 At4g19420 0.712183 2184 similar to ADP-ribosylation factor gb|AAD17207; similar toESTs 2E−80 At1g10630 0.67 2185 2186 hypothetical protein 0 At1g044200.67 2187 2188 putative protein 0 At4g26710 0.62 2189 2190 putativeprotein 0 At4g34630 0.72 2191 2192 latex protein 0 At1g70890 0.29 21932194 RCc3 - like protein 0 At4g22490 0.57 2195 2196 hypothetical protein5E−53 At1g20450 0.49 2197 2198 glucosyltransferase-like protein 3E−31At5g22740 0.65 2199 2200 glutathione S-transferase 0 At2g29450 0.52 22012202 putative protein 0 At3g44450 0.59 2203 2204 cysteine synthase 0At5g28020 0.6 2205 2206 ATP synthase 0 At4g04640 0.57 2207 2208 40Sribosomal protein S14 1E−25 At2g36160 0.67 2209 2210 putative protein 0At4g19100 0.76 2211 2212 K Efflux antiporter KEA1 0 At1g01790 0.65 22132214 hypothetical protein 1E−169 At2g42980 0.66 2215 2216 cytochromeP450 like protein 1E−01 At4g36380 0.48 2217 2218 unknown protein 8E−64At2g01520 0.23 2219 2220 hypothetical protein 1E−157 At1g07130 0.66 22212222 putative protein 5E−04 At5g09620 0.62 2223 2224 unknown protein 0At1g08470 0.66 2225 2226 putative protein 6E−37 At3g54600 0.7 2227 2228DnaJ - like protein 1E−68 At4g39960 0.52 2229 2230 putative proteinphosphatase 2C 1E−161 At1g78200 0.72 2231 2232 biotin synthase (Bio B) 0At2g43360 0.67 2233 2234 unknown protein 3E−69 At3g17510 0.55 2235 2236high mobility group protein 2-like 1E−107 At3g51880 0.66 2237 2238putative proline-rich protein 0 At2g21140 0.57 2239 2240 cyclin delta-30 At4g34160 0.74 2241 2242 serine carboxypeptidase II - like protein 0At4g30810 0.77 2243 2244 unknown protein 0 At1g67330 0.7 2245 2246putative protein 7E−93 At3g56010 0.7 2247 2248 GTP-binding protein LepAhomolog 0 At5g08650 0.76 2249 2250 unknown protein 0 At3g10420 0.42 22512252 putative protein 0 At3g51510 0.58 2253 2254 putative protein 0At3g45870 0.73 2255 2256 putative enolase 0 At1g74030 0.65 2257 2258putative protein 3E−05 At5g11680 0.71 2259 2260 putative protein 0At5g26280 0.58 2261 2262 O-methyltransferase, putative 0 At1g21100 0.632263 2264 beta-1,3-glucanase class I precursor 0 At4g16260 0.51 22652266 protein phosphatase 2C (PP2C) 2E−27 At3g11410 0.67 2267 2268 rootcap protein 2-like protein 1E−174 At5g54370 0.75 2269 2270 putativeadenosine phosphosulfate kinase 0 At2g14750 0.47 2271 2272 putativeprotein 0 At4g30010 0.73 2273 2274 putative uroporphyrinogendecarboxylase 2E−9 At2g40490 0.75 2275 2276 putative protein 1E−151At3g57400 0.71 2277 2278 branched-chain amino acid aminotransferase,putative 1E−56 At3g19710 0.3 2279 2280 copia-like retroelement polpolyprotein 0 At2g19830 0.72 2281 2282 neoxanthin cleavage enzyme-likeprotein 0 At4g19170 0.38 2283 2284 hypothetical protein 0 At1g31860 0.72285 2286 unknown protein 0 At2g26570 0.61 2287 2288 asparaginesynthetase ASN3 0 At5g10240 0.72 2289 2290 hypothetical protein 1E−80At1g64770 0.56 2291 2292 expansin S2 precursor, putative 1E−114At1g20190 0.51 2293 2294 5′-adenylylsulfate reductase 0 At4g04610 0.432295 2296 putative protein 9E−02 At3g59680 0.71 2297 2298 putative MYBfamily transcription factor 4E−31 At2g37630 0.73 2299 2300 Putativeprotein kinase 3E−23 At1g51850 0.6 2301 2302 putative protein 0At5g15910 0.76 2303 2304 AALP protein 0 At5g60360 0.63 2305 2306putative galactinol synthase 0 At2g47180 0.69 2307 2308 cyanohydrinlyase like protein 0 At4g16690 0.56 2309 2310 putative protein 0At5g03880 0.57 2311 2312 putative glucosyltransferase 0 At2g30150 0.732313 2314 cysteine endopeptidase precursor - like protein 0 At3g483500.65 2315 2316 unknown protein 1E−122 At3g07700 0.7 2317 2318 putativeperoxiredoxin 2E−86 At3g26060 0.76 2319 2320 MAPKK 0 At1g73500 0.58 23212322 hypothetical protein 7E−74 At1g64780 0.52 2323 2324 UDP glucose:flavonoid 3-o-glucosyltransferase, putative 2E−90 At1g30530 0.59 23252326 hypothetical protein 0 At4g02800 0.55 2327 2328 oxidoreductase -like protein 0 At3g55290 0.65 2329 2330 hypothetical protein 0 At1g506700.73 2331 2332 carnitine/acylcarnitine translocase-like protein 0At5g46800 0.58 2333 2334 MATH protein 1E−169 At4g00780 0.57 2335 2336unknown protein 0 At1g22630 0.76 2337 2338 cytochrome P450-like protein0 At4g37330 0.72 2339 2340 putative endo-1,4-beta glucanase 8E−36At4g02290 0.62 2341 2342 hevein-like protein precursor 0E+00 At3g047200.75 2343 2344 leucine zipper-containing protein AT103 1E−139 At3g569400.63 2345 2346 delta-1-pyrroline-5-carboxylate synthetase 0 At3g556100.69 2347 2348 remorin 0 At2g45820 0.76 2349 2350 putative protein 0At5g22460 0.48 2351 2352 putative lectin 0 At3g16530 0.43 2353 2354putative protein 9E−29 At5g26260 0.52 2355 2356 peptidylprolyl isomeraseROC4 0 At3g62030 0.61 2357 2358 O-methyltransferase, putative 0At1g21130 0.63 2359 2360 putative zinc finger protein 0 At4g38960 0.722361 2362 putative hydroxyproline-rich glycoprotein 1E−173 At1g139300.58 2363 2364 putative protein 1 photosystem II oxygen-evolving complex0 At3g50820 0.65 2365 2366 hypothetical protein 0 At1g66700 0.63 23672368 unknown protein 0 At1g52870 0.43 2369 2370 heat shock protein 90 0At5g56010 0.75 2371 2372 Overlap with bases 87, 142-90, 425 of ‘IGF’ BACclone F9K20, 1E−115 At1g78570 0.63 accession 2373 2374 phosphoglyceratekinase, putative 1E−120 At3g12780 0.73 2375 2376 putative lectin 1E−25At3g16400 0.4 2377 2378 profilin 2 0 At4g29350 0.77 2379 2380 HSPassociated protein like 5E−16 At4g22670 0.75 2381 2382 putative celldivision control protein, cdc2 kinase 1E−75 At1g20930 0.72 2383 2384putative protein 1E−107 At5g08050 0.65 2385 2386 ribosomal protein S27 0At5g47930 0.77 2387 2388 vacuolar H+-transporting ATPase 16K chain 0At4g34720 0.76 2389 2390 expansin At-EXP5 3E−82 At3g29030 0.52 2391 2392similar to cold acclimation protein WCOR413 [Triticum aestivum] 0At2g15970 0.74 2393 2394 chloroplast membrane protein (ALBINO3) 1E−159At2g28800 0.72 2395 2396 putative thioredoxin 1E−102 At1g08570 0.55 23972398 unknown protein 0 At1g08380 0.65 2399 2400 hypothetical protein 0At1g07180 0.53 2401 2402 putative flavonol sulfotransferase 0 At1g740900.69 2403 2404 possible apospory-associated like protein 0 At4g259000.71 2405 2406 glycolate oxidase, putative 0 At3g14420 0.71 2407 2408putative peroxidase ATP2a 0 At2g37130 0.75 2409 2410 putative protein1E−154 At4g21860 0.75 2411 2412 hydroxypyruvate reductase (HPR) 0At1g68010 0.74 2413 2414 photosystem I reaction centre subunit psaNprecursor (PSI-N) 0 At5g64040 0.49 2415 2416 plastid ribosomal proteinS6, putative 0 At1g64510 0.6 2417 2418 methylenetetrahydrofolatereductase MTHFR1 0 At3g59970 0.72 2419 2420 putative photosystem Ireaction center subunit II precursor 0 At1g03130 0.55 2421 2422 unknownprotein 0 At3g10940 0.64 2423 2424 fumarate hydratase 0 At5g50950 0.432425 2426 Lil3 protein 0 At5g47110 0.73 2427 2428 homeobox gene ATH1 0At4g32980 0.76 2429 2430 putative lectin 3E−20 At3g16390 0.43 2431 2432COP1-interacting protein 7 (CIP7) 1E−07 At4g27430 0.67 2433 2434putative acyl-CoA synthetase 0 At2g47240 0.51 2435 2436 unknown protein0 At2g01590 0.68 2437 2438 hydroxymethyltransferase 0 At4g13930 0.722439 2440 hypothetical protein 1E−164 At1g69490 0.27 2441 2442 SNF1related protein kinase (ATSRPK1) 1E−170 At3g23000 0.49 2443 2444mevalonate diphosphate decarboxylase 6E−68 At2g38700 0.71 2445 2446putative flavonol sulfotransferase 0 At1g74090 0.69 2447 2448 proteinphosphatase 2C (AtP2C-HA) 0 At1g72770 0.59 2449 2450 cinnamoyl-CoAreductase - like protein 0 At4g30470 0.72 2451 2452O-methyltransferase - like protein 0 At4g35160 0.5 2453 2454 pyruvatedehydrogenase E1 alpha subunit 0 At1g01090 0.77 2455 2456 putativechlorophyll A-B binding protein 0 At3g27690 0.49 2457 2458 putativeUDP-N-acetylglucosamine pyrophosphorylase 0 At2g35020 0.69 2459 2460putative protein 1E−121 At4g05590 0.75 2461 2462 Ca2+-dependentmembrane-binding protein annexin 0 At1g35720 0.41 2463 2464 hypotheticalprotein 0 At2g35760 0.51 2465 2466 hypothetical protein 2E−15 At1g188400.71 2467 2468 hypothetical protein 0 At1g51140 0.53 2469 2470 aromaticamino-acid decarboxylase - like protein 0 At4g28680 0.73 2471 2472unknown protein 3E−72 At2g35830 0.49 2473 2474 hypothetical protein 0At1g78690 0.66 2475 2476 putative elongation factor P (EF-P) 0 At3g087400.74 2477 2478 unknown protein 0 At1g22750 0.76 2479 2480 putativeprotein 0 At3g63160 0.45 2481 2482 unknown protein 1E−150 At3g26510 0.552483 2484 aldo/keto reductase-like protein 0 At5g53580 0.69 2485 2486glycine decarboxylase complex H-protein 0 At2g35370 0.53 2487 2488thioredoxin (clone GIF1) (pir||S58118) 3E−14 At5g42980 0.53 2489 2490putative protein 1E−93 At4g28020 0.52 2491 2492 hypothetical protein 0At1g18870 0.71 2493 2494 vegetative storage protein Vsp2 0 At5g247700.43 2495 2496 putative protein 3E−75 At4g17560 0.66 2497 2498 NBD-likeprotein (gb|AAD20643.1) 0E+00 At5g44110 0.58 2499 2500 photosystem Isubunit V precursor, putative 1E−119 At1g55670 0.56 2501 2502 putativethaumatin 2E−36 At2g28790 0.64 2503 2504 hyoscyamine 6-dioxygenasehydroxylase, putative 0 At1g35190 0.71 2505 2506 H-protein promoterbinding factor-like protein 0 At5g62430 0.51 2507 2508 putative protein0 At4g04840 0.52 2509 2510 endo-xyloglucan transferase - like protein 0At4g37800 0.68 2511 2512 vitamine c-2 0 At4g26850 0.33 2513 2514hypothetical protein 0 At3g12340 0.69 2515 2516 putativeacetone-cyanohydrin lyase 0 At2g23610 0.68 2517 2518 putativetranscription factor 0 At1g71030 0.36 2519 2520 hypothetical protein1E−128 At1g19000 0.74 2521 2522 putative xyloglucanendo-transglycosylase 7E−27 At2g36870 0.4 2523 2524 hypothetical protein3E−51 At1g58080 0.77 2525 2526 putative protein 1E−167 At5g36800 0.652527 2528 putative protein 1E−157 At4g30530 0.65 2529 2530cinnamyl-alcohol dehydrogenase ELI3-1 0 At4g37980 0.54 2531 2532putative CONSTANS-like B-box zinc finger protein 0 At2g47890 0.72 25332534 unknown protein 1E−123 At1g53480 0.6 2535 2536 protein phosphatase2C-like protein 2E−55 At4g28400 0.72 2537 2538 putative protein 0At5g60680 0.57 2539 2540 farnesyl-pyrophosphate synthetase FPS2 0At4g17190 0.76 2541 2542 soluble inorganic pyrophosphatase, putative 0At1g01050 0.59 2543 2544 putative nematode-resistance protein 1E−117At2g40000 0.34 2545 2546 putative AP2 domain transcription factor 0At2g23340 0.74 2547 2548 putative myo-inositol monophosphatase 3E−17At3g02870 0.6 2549 2550 putative isoamylase 0 At1g03310 0.74 2551 2552phosphate transporter (AtPT2) 0 At2g38940 0.76 2553 2554 putativedisease resistance response protein 0 At4g11190 0.68 2555 2556 unknownprotein 0 At2g45600 0.55 2557 2558 peroxidase ATP13a 0 At5g17820 0.72559 2560 unknown protein 0 At1g26920 0.74 2561 2562 putativemitochondrial carrier protein 0 At2g47490 0.69 2563 2564 actindepolymerizing factor 3 - like protein 1E−136 At5g59880 0.64 2565 2566putative protein transport protein SEC23 1E−149 At2g21630 0.73 2567 2568unknown protein 2E−30 At2g44310 0.74 2569 2570 putative protein 0At4g21570 0.69 2571 2572 putative steroid binding protein 0 At2g249400.57 2573 2574 putative lipid transfer protein 0 At2g15050 0.49 25752576 hypothetical protein 0 At4g15510 0.75 2577 2578 unknown protein3E−47 At3g25690 0.56 2579 2580 40S ribosomal protein S19 - like 0At5g28060 0.73 2581 2582 putative auxin-regulated protein 0 At2g212100.56 2583 2584 unknown protein 0 At1g19350 0.71 2585 2586 unknownprotein 1E−136 At1g07700 0.71 2587 2588 50S ribosomal protein L27 0E+00At5g40950 0.7 2589 2590 unknown protein 1E−105 At2g46540 0.69 2591 2592ATP-sulfurylase 0 At4g14680 0.72 2593 2594 hypothetical protein 1E−107At3g18890 0.64 2595 2596 putative protein 0 At3g59780 0.62 2597 2598cytochrome P450 monooxygenase - like protein 0 At4g37410 0.56 2599 2600hypothetical protein 2E−86 At1g61890 0.36 2601 2602ubiquitin-conjugating enzyme, putative 0 At3g20060 0.66 2603 2604hypothetical protein 0 At1g20810 0.74 2605 2606 hypothetical protein 0At2g15020 0.45 2607 2608 unknown protein 0 At1g55480 0.52 2609 2610 UDPglucose: flavonoid 3-o-glucosyltransferase - like protein 0 At5g170500.56 2611 2612 hypothetical protein 0 At3g23670 0.69 2613 2614 putativeprotein 0 At4g34920 0.69 2615 2616 unknown protein 1E−100 At2g36630 0.712617 2618 unknown protein 6E−94 At1g56580 0.63 2619 2620 HSR201 likeprotein 0 At4g15390 0.75 2621 2622 heme oxygenase 1 (HO1) 0 At2g266700.74 2623 2624 putative beta-glucosidase 0 At4g27820 0.46 2625 2626unknown protein 1E−122 At1g68440 0.45 2627 2628 predicted protein 0At4g22820 0.54 2629 2630 putative kinesin heavy chain 0 At2g22610 0.722631 2632 putative protein 0 At4g27860 0.61 2633 2634 unknown protein 0At2g37240 0.76 2635 2636 unknown protein 0 At1g30070 0.76 2637 2638WD-repeat protein - like protein 0 At4g33270 0.57 2639 2640 unknownprotein 0 At1g32220 0.6 2641 2642 hypothetical protein 0 At4g22920 0.732643 2644 putative amino acid transporter protein 0 At3g11900 0.67 26452646 endo-beta-1,4-glucanase, putative 0 At1g64390 0.5 2647 2648hypothetical protein 0 At1g18060 0.6 2649 2650 hypothetical protein1E−114 At4g39820 0.7 2651 2652 putative protein 1E−62 At5g27290 0.6 26532654 putative protein 1E−133 At3g48200 0.46 2655 2656 hypotheticalprotein 1E−173 At1g64500 0.51 2657 2658 putative ribonuclease, RNS2 0At2g39780 0.6 2659 2660 thioredoxin f1 0 At3g02730 0.59 2661 2662unknown protein 0 At2g20670 0.67 2663 2664 cytochrome P450-like protein0 At5g48000 0.45 2665 2666 subtilisin proteinase - like 1E−105 At4g216500.31 2667 2668 photoassimilate-responsive protein PAR-1b - like protein0E+00 At3g54040 0.76 2669 2670 putative dTDP-glucose 4-6-dehydratase 0At2g27860 0.45 2671 2672 hypothetical protein 0 At1g51700 0.43 2673 2674early light-induced protein 0 At3g22840 0.65 2675 2676 hypotheticalprotein 0 At1g32060 0.42 2677 2678 unknown protein 0 At2g34860 0.69 26792680 peroxidase ATP3a (emb|CAA67340.1) 4E−10 At5g64100 0.49 2681 2682putative protein 0 At5g06770 0.67 2683 2684 hypothetical protein 0At2g16860 0.57 2685 2686 annexin 0 At5g65020 0.61 2687 2688 thioredoxin,putative 0 At1g50320 0.63 2689 2690 putative protein 0 At5g17360 0.662691 2692 nucleoside diphosphate kinase 3 (ndpk3) 0 At4g11010 0.76 26932694 unknown protein 0 At5g62550 0.64 2695 2696 putative protein 0At4g12000 0.62 2697 2698 cell division protease FtsH, putative 0At1g06430 0.65 2699 2700 unknown protein 0 At1g74880 0.41 2701 2702putative protein 0 At5g56540 0.61 2703 2704 unknown protein 0 At1g687800.61 2705 2706 mipC protein - like (aquaporin) 0 At5g60660 0.64 27072708 Oxygen-evolving enhancer protein 3 precursor - like protein 0At4g05180 0.64 2709 2710 cytochrome P450, putative 0 At3g26180 0.74 27112712 putative protein 1E−126 At5g22210 0.74 2741 2742 unknown proteinAt1g45200 3.91 2743 2744 unknown protein, putative protease inhibitorAt5g43580 2.58 2745 2746 putative protein At5g03540 2.21 2747 2748putative WD repeat protein At3g15880 2.38 2749 2750 putative proteaseinhibitor Dr4 At1g73330 10.30 2751 2752 putative auxin regulated proteinAt2g46690 2.86 2753 2754 translation initiation factor like proteinAt5g54940 2.15 2755 pseudogene At2g04110 2.07

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1. A method to alter one or more plant characteristics, said methodcomprising modifying, in a plant, expression of one or more nucleicacids and/or modifying level and/or activity of one or more proteins,which nucleic acids and/or proteins are essentially similar to any oneof SEQ ID NO 1 to 2755, and wherein said one or more plantcharacteristics are altered relative to corresponding wild type plants.2. A method according to claim 1, wherein said altered plantcharacteristic is selected from any one or more of the following:altered development, altered growth, increased yield and/or biomass,enhanced survival capacity, enhanced stress tolerance, altered plantarchitecture, altered plant physiology, altered plant biochemistry,altered metabolism, altered DNA synthesis, altered DNA modification,altered endoreduplication, altered cell cycle, altered cell wallbiogenesis, altered transcription regulation, altered signaltransduction, altered storage lipid mobilization and/or alteredphotosynthesis, each relative to corresponding wild type plants.
 3. Amethod according to claim 2, wherein said altered metabolism comprisesaltered nitrogen and/or altered carbon metabolism.
 4. A method accordingto claim 2, wherein said increased yield and/or biomass, comprisesincreased seed yield.
 5. A recombinant nucleic acid comprising: (a) oneor more nucleic acid sequences essentially similar to any one of SEQ IDNO 1 to 2755 or the complement strand thereof; optionally operablylinked to (b) a regulatory sequence, and optionally operably linked to(c) a transcription termination sequence
 6. A recombinant nucleic acidaccording to claim 5, wherein said regulatory sequence is aplant-expressible promoter.
 7. A recombinant nucleic acid according toclaims 6, wherein said plant-expressible promoter is any one of thepromoters listed in Table I, II, III or IV.
 8. A method for making atransgenic plant or plant cell having one or more altered plantcharacteristics when compared to the corresponding wild-typecharacteristics, said method comprising introduction of a recombinantnucleic acid according to claim 5 into said plant or plant cell.
 9. Amethod according to claim 8, wherein said recombinant nucleic acid isstably integrated into the genome of said plant.
 10. A method accordingto claim 1, comprising overexpression of one or more nucleic acidsessentially similar to any one of SEQ ID NO 1 to
 2755. 11. A methodaccording to claim 1, comprising downregulation of expression of one ormore nucleic acids essentially similar to any one of SEQ ID NO 1 to2755.
 12. A transgenic plant having one or more altered characteristicswhen compared to the corresponding wild-type plant, characterized inthat said plant has modified expression of one or more nucleic acidsand/or modified level and/or activity of one or more proteins, saidnucleic acid and/or protein being essentially similar to any one of SEQID NO 1 to
 2755. 13. A transgenic plant obtainable by a method accordingto claim
 1. 14. A transgenic plant comprising an isolated nucleic acidand/or protein sequence essentially similar to any one of SEQ ID NO 1 to2755.
 15. An ancestor, progeny, or any plant part, particularly aharvestable part, of a transgenic plant of claim
 12. 16. A host cellhaving one or more altered characteristics when compared to thecorresponding wild-type host cell, characterized in that said host cellhas modified expression of one or more nucleic acids and/or modifiedlevel and/or activity of one or more proteins, said nucleic acid and/orprotein being essentially similar to any one of SEQ ID NO 1 to
 2755. 17.Use of a nucleic acid sequence or protein essentially similar to any oneof SEQ ID NO 1 to 2755, for altering one or more plant characteristics.18. A method for the production of plants with one or more alteredcharacteristics when compared to the corresponding wild-type plants,which method comprises the use of a nucleic acid sequence essentiallysimilar to any of SEQ ID NO 1 to 2755 in marker assisted breeding.
 19. Amethod for the production of plants with one or more alteredcharacteristics when compared to the corresponding wild-type plants,which method comprises the use of a nucleic acid sequence essentiallysimilar to any of SEQ ID NO 1 to 2755 in conventional breeding.
 20. Aplant obtainable by the methods according to claim
 18. 21. Use of anucleic acid and/or a protein essentially similar to any one of SEQ IDNO 1 to 2755 as a growth regulator.
 22. A growth regulating compositioncomprising a nucleic acid and/or a protein essentially similar to anyone of SEQ ID NO 1 to
 2755. 23. A method for the production of a growthregulator, comprising the production of a nucleic acid and/or a proteinessentially similar to any one of SEQ ID NO 1 to
 2755. 24. Method forthe production of enzymes and/or pharmaceuticals, which method comprisesmodifying expression of a nucleic acid, and/or modifying level and/oractivity of a protein, said nucleic acid and/or protein beingessentially similar to any one of SEQ ID NO 1 to
 2755. 25. Use of plantsaccording to claim 11 to 14, for the production of enzymes and/orpharmaceuticals.
 26. Enzymes and pharmaceuticals produced according tothe method of claim
 24. 27. Use of a nucleic acid or a proteinessentially similar to any one of SEQ ID NO 1 to 2755, as a therapeuticagent, a diagnostic means, a kit or plant effective agent.
 28. Atherapeutic composition comprising a nucleic acid and/or a proteinessentially similar to any one of SEQ ID NO 1 to
 2755. 29. A diagnosticcomposition comprising a nucleic acid and/or a protein essentiallysimilar to any one of SEQ ID NO 1 to
 2755. 30. A kit comprising anucleic acid and/or a protein essentially similar to any one of SEQ IDNO 1 to
 2755. 31. A plant effective agent comprising a nucleic acidand/or a protein essentially similar to any one of SEQ ID NO 1 to 2755.32. Method for the manufacturing of a therapeutic composition, adiagnostic composition, a kit or a plant effective agent, comprising theproduction of a sequence essentially similar to any one of SEQ ID NO 1to
 2755. 33. A food product derived from a plant or host cell accordingto any one of claim 12 to
 16. 34. Use of a food product according toclaim 33 in animal feed or food.
 35. Method for the production of a foodor feed product, which method comprises modifying expression of anucleic acid, and/or modifying level and/or activity of a protein, saidnucleic acid and/or protein being essentially similar to any one of SEQID NO 1 to
 2755. 36. Use of a nucleic acid or a protein essentiallysimilar to any one of SEQ ID NO 1 to 2755 as a positive or negativeselectable marker during transformation of cells or tissues or duringcell procedures.
 37. Use according to claim 36, wherein said cell isderived from a plant, animal, bacterium, fungus, yeast, insect, algae.38. An isolated nucleic acid comprising one or more of the regulatoryelements upstream of the start codon of any of the nucleic acidsrepresented by SEQ ID NO 1 to
 2755. 39. An isolated nucleic acidaccording to claim 38, wherein said regulatory element is the naturalpromoter of any one of said nucleic acids represented by SEQ ID NO 1 to2755.